diff --git a/CMake/External_Caffe.cmake b/CMake/External_Caffe.cmake
index d74aa5a3..9488898f 100644
--- a/CMake/External_Caffe.cmake
+++ b/CMake/External_Caffe.cmake
@@ -75,33 +75,24 @@ endif()
 set( CAFFE_PROTOBUF_ARGS )
 
 if(fletch_ENABLE_Protobuf)
-  get_system_library_name( protobuf protobuf_libname )
-  get_system_library_name( protobuf-lite protobuf-lite_libname )
-  get_system_library_name( protoc protoc_libname )
-
-  set( CAFFE_PROTOBUF_ARGS
-    -DPROTOBUF_INCLUDE_DIR:PATH=${fletch_BUILD_INSTALL_PREFIX}/include
-    -DPROTOBUF_LIBRARY:PATH=${fletch_BUILD_INSTALL_PREFIX}/lib/${protobuf_libname}
-    -DPROTOBUF_LIBRARY_DEBUG:PATH=${fletch_BUILD_INSTALL_PREFIX}/lib/${protobuf_libname}
-    -DPROTOBUF_LITE_LIBRARY:PATH=${fletch_BUILD_INSTALL_PREFIX}/lib/${protobuf-lite_libname}
-    -DPROTOBUF_LITE_LIBRARY_DEBUG:PATH=${fletch_BUILD_INSTALL_PREFIX}/lib/${protobuf-lite_libname}
-    -DPROTOBUF_PROTOC_EXECUTABLE:PATH=${fletch_BUILD_INSTALL_PREFIX}/bin/protoc
-    -DPROTOBUF_PROTOC_LIBRARY:PATH=${fletch_BUILD_INSTALL_PREFIX}/lib/${protoc_libname}
-    -DPROTOBUF_PROTOC_LIBRARY_DEBUG:PATH=${fletch_BUILD_INSTALL_PREFIX}/lib/${protoc_libname}
-    )
+  set(protobuf_include ${fletch_BUILD_INSTALL_PREFIX}/include)
+  set(protobuf_exe ${fletch_BUILD_INSTALL_PREFIX}/bin/protoc)
 else()
-  set( CAFFE_PROTOBUF_ARGS
-    -DPROTOBUF_INCLUDE_DIR:PATH=${PROTOBUF_INCLUDE_DIR}
-    -DPROTOBUF_LIBRARY:PATH=${PROTOBUF_LIBRARY}
-    -DPROTOBUF_LIBRARY_DEBUG:PATH=${PROTOBUF_LIBRARY_DEBUG}
-    -DPROTOBUF_LITE_LIBRARY:PATH=${PROTOBUF_LITE_LIBRARY}
-    -DPROTOBUF_LITE_LIBRARY_DEBUG:PATH=${PROTOBUF_LITE_LIBRARY_DEBUG}
-    -DPROTOBUF_PROTOC_EXECUTABLE:PATH=${PROTOBUF_PROTOC_EXECUTABLE}
-    -DPROTOBUF_PROTOC_LIBRARY:PATH=${PROTOBUF_PROTOC_LIBRARY}
-    -DPROTOBUF_PROTOC_LIBRARY_DEBUG:PATH=${PROTOBUF_PROTOC_LIBRARY_DEBUG}
-    )
+  set(protobuf_include ${PROTOBUF_INCLUDE_DIR})
+  set(protobuf_exe ${PROTOBUF_PROTOC_EXECUTABLE})
 endif()
 
+set( CAFFE_PROTOBUF_ARGS
+  -DPROTOBUF_INCLUDE_DIR:PATH=${protobuf_include}
+  -DPROTOBUF_LIBRARY:PATH=${PROTOBUF_LIBRARY}
+  -DPROTOBUF_LIBRARY_DEBUG:PATH=${PROTOBUF_LIBRARY}
+  -DPROTOBUF_LITE_LIBRARY:PATH=${PROTOBUF_LITE_LIBRARY}
+  -DPROTOBUF_LITE_LIBRARY_DEBUG:PATH=${PROTOBUF_LITE_LIBRARY}
+  -DPROTOBUF_PROTOC_EXECUTABLE:PATH=${protobuf_exe}
+  -DPROTOBUF_PROTOC_LIBRARY:PATH=${PROTOBUF_PROTOC_LIBRARY}/
+  -DPROTOBUF_PROTOC_LIBRARY_DEBUG:PATH=${PROTOBUF_PROTOC_LIBRARY}
+  )
+
 if(fletch_ENABLE_OpenCV)
   set( CAFFE_OPENCV_ARGS
     -DOpenCV_DIR:PATH=${fletch_BUILD_PREFIX}/src/OpenCV-build
diff --git a/CMake/External_Caffe_Segnet.cmake b/CMake/External_Caffe_Segnet.cmake
index 1437a6cf..c8bc7640 100644
--- a/CMake/External_Caffe_Segnet.cmake
+++ b/CMake/External_Caffe_Segnet.cmake
@@ -76,33 +76,24 @@ endif()
 set( CAFFE_SEGNET_PROTOBUF_ARGS )
 
 if(fletch_ENABLE_Protobuf)
-  get_system_library_name( protobuf protobuf_libname )
-  get_system_library_name( protobuf-lite protobuf-lite_libname )
-  get_system_library_name( protoc protoc_libname )
-
-  set( CAFFE_SEGNET_PROTOBUF_ARGS
-    -DPROTOBUF_INCLUDE_DIR:PATH=${fletch_BUILD_INSTALL_PREFIX}/include
-    -DPROTOBUF_LIBRARY:PATH=${fletch_BUILD_INSTALL_PREFIX}/lib/${protobuf_libname}
-    -DPROTOBUF_LIBRARY_DEBUG:PATH=${fletch_BUILD_INSTALL_PREFIX}/lib/${protobuf_libname}
-    -DPROTOBUF_LITE_LIBRARY:PATH=${fletch_BUILD_INSTALL_PREFIX}/lib/${protobuf-lite_libname}
-    -DPROTOBUF_LITE_LIBRARY_DEBUG:PATH=${fletch_BUILD_INSTALL_PREFIX}/lib/${protobuf-lite_libname}
-    -DPROTOBUF_PROTOC_EXECUTABLE:PATH=${fletch_BUILD_INSTALL_PREFIX}/bin/protoc
-    -DPROTOBUF_PROTOC_LIBRARY:PATH=${fletch_BUILD_INSTALL_PREFIX}/lib/${protoc_libname}
-    -DPROTOBUF_PROTOC_LIBRARY_DEBUG:PATH=${fletch_BUILD_INSTALL_PREFIX}/lib/${protoc_libname}
-    )
+  set(protobuf_include ${fletch_BUILD_INSTALL_PREFIX}/include)
+  set(protobuf_exe ${fletch_BUILD_INSTALL_PREFIX}/bin/protoc)
 else()
-  set( CAFFE_SEGNET_PROTOBUF_ARGS
-    -DPROTOBUF_INCLUDE_DIR:PATH=${PROTOBUF_INCLUDE_DIR}
-    -DPROTOBUF_LIBRARY:PATH=${PROTOBUF_LIBRARY}
-    -DPROTOBUF_LIBRARY_DEBUG:PATH=${PROTOBUF_LIBRARY_DEBUG}
-    -DPROTOBUF_LITE_LIBRARY:PATH=${PROTOBUF_LITE_LIBRARY}
-    -DPROTOBUF_LITE_LIBRARY_DEBUG:PATH=${PROTOBUF_LITE_LIBRARY_DEBUG}
-    -DPROTOBUF_PROTOC_EXECUTABLE:PATH=${PROTOBUF_PROTOC_EXECUTABLE}
-    -DPROTOBUF_PROTOC_LIBRARY:PATH=${PROTOBUF_PROTOC_LIBRARY}
-    -DPROTOBUF_PROTOC_LIBRARY_DEBUG:PATH=${PROTOBUF_PROTOC_LIBRARY_DEBUG}
-  )
+  set(protobuf_include ${PROTOBUF_INCLUDE_DIR})
+  set(protobuf_exe ${PROTOBUF_PROTOC_EXECUTABLE})
 endif()
 
+set( CAFFE_SEGNET_PROTOBUF_ARGS
+  -DPROTOBUF_INCLUDE_DIR:PATH=${protobuf_include}
+  -DPROTOBUF_LIBRARY:PATH=${PROTOBUF_LIBRARY}
+  -DPROTOBUF_LIBRARY_DEBUG:PATH=${PROTOBUF_LIBRARY}
+  -DPROTOBUF_LITE_LIBRARY:PATH=${PROTOBUF_LITE_LIBRARY}
+  -DPROTOBUF_LITE_LIBRARY_DEBUG:PATH=${PROTOBUF_LITE_LIBRARY}
+  -DPROTOBUF_PROTOC_EXECUTABLE:PATH=${protobuf_exe}
+  -DPROTOBUF_PROTOC_LIBRARY:PATH=${PROTOBUF_PROTOC_LIBRARY}/
+  -DPROTOBUF_PROTOC_LIBRARY_DEBUG:PATH=${PROTOBUF_PROTOC_LIBRARY}
+  )
+
 if(fletch_ENABLE_OpenCV)
   set( CAFFE_SEGNET_OPENCV_ARGS
     -DOpenCV_DIR:PATH=${fletch_BUILD_PREFIX}/src/OpenCV-build
@@ -176,7 +167,6 @@ if(fletch_ENABLE_HDF5)
     get_system_library_name( hdf5_cpp_debug hdf5_cpp_libname )
     get_system_library_name( hdf5_hl_cpp_debug hdf5_hl_cpp_libname )
 
-
   else()
 
     get_system_library_name( hdf5 hdf5_libname )
@@ -270,7 +260,6 @@ else()
     )
 endif()
 
-
 set (Caffe_Segnet_PATCH_DIR "${fletch_SOURCE_DIR}/Patches/Caffe_Segnet/${Caffe_Segnet_version}")
 if (EXISTS ${Caffe_Segnet_PATCH_DIR})
   set(
diff --git a/CMake/External_Protobuf.cmake b/CMake/External_Protobuf.cmake
index e98eff06..7bcc0601 100644
--- a/CMake/External_Protobuf.cmake
+++ b/CMake/External_Protobuf.cmake
@@ -1,52 +1,84 @@
-if (WIN32)
-  # Build option for windows not yet generated
-  message( FATAL_ERROR "Protobuf on windows not yet supported" )
-endif()
 
-# Check that python and protobuf versions are compatible
-if(fletch_BUILD_WITH_PYTHON AND fletch_ENABLE_Protobuf)
-  # Note the python protobuf wrapper is not installed here.
-  # Instead it must be installed via `pip install protobuf`
-  if (${Protobuf_version} LESS 3.0 AND fletch_PYTHON_MAJOR_VERSION MATCHES "^3.*")
-    message(ERROR " Must use Protobuf >= 3.x with Python 3.x")
+set(protobuf_BUILD_SHARED_LIBS "OFF")
+if (Protobuf_SELECT_VERSION STREQUAL "3.9.0")
+  ExternalProject_Add(Protobuf
+#    PREFIX protobuf
+    URL ${Protobuf_url}
+    URL_MD5 ${Protobuf_md5}
+    SOURCE_SUBDIR ./cmake
+    ${COMMON_EP_ARGS}
+    ${COMMON_CMAKE_EP_ARGS}
+    CMAKE_ARGS
+       ${COMMON_CMAKE_ARGS}
+       -Dprotobuf_BUILD_TESTS:BOOL=OFF
+       -Dprotobuf_BUILD_EXAMPLES:BOOL=${protobuf_BUILD_SHARED_LIBS}
+       -Dprotobuf_BUILD_SHARED_LIBS:BOOL=OFF
+       -Dprotobuf_MSVC_STATIC_RUNTIME:BOOL=OFF#Don't change MSVC runtime settings (/MD or /MT)
+       -DCMAKE_POSITION_INDEPENDENT_CODE:BOOL=TRUE
+       -Dprotobuf_WITH_ZLIB:BOOL=OFF
+    )
+elseif (NOT WIN32)
+  set (Protobuf_PATCH_DIR ${fletch_SOURCE_DIR}/Patches/Protobuf/${Protobuf_SELECT_VERSION})
+  if (EXISTS ${Protobuf_PATCH_DIR})
+    set(Protobuf_PATCH_COMMAND ${CMAKE_COMMAND}
+      -DProtobuf_PATCH_DIR=${Protobuf_PATCH_DIR}
+      -DProtobuf_SOURCE_DIR=${fletch_BUILD_PREFIX}/src/Protobuf
+      -P ${Protobuf_PATCH_DIR}/Patch.cmake)
+  else()
+    set(Protobuf_PATCH_COMMAND "")
   endif()
-endif()
-
-
-
-set (Protobuf_PATCH_DIR ${fletch_SOURCE_DIR}/Patches/Protobuf/${Protobuf_SELECT_VERSION})
-if (EXISTS ${Protobuf_PATCH_DIR})
-  set(Protobuf_PATCH_COMMAND ${CMAKE_COMMAND}
-    -DProtobuf_PATCH_DIR=${Protobuf_PATCH_DIR}
-    -DProtobuf_SOURCE_DIR=${fletch_BUILD_PREFIX}/src/Protobuf
-    -P ${Protobuf_PATCH_DIR}/Patch.cmake)
-else()
-  set(Protobuf_PATCH_COMMAND "")
-endif()
-
 
-Fletch_Require_Make()
-ExternalProject_Add(Protobuf
-  URL ${Protobuf_url}
-  URL_MD5 ${Protobuf_md5}
-  ${COMMON_EP_ARGS}
-  PATCH_COMMAND ${CMAKE_COMMAND}
+  Fletch_Require_Make()
+  ExternalProject_Add(Protobuf
+    URL ${Protobuf_url}
+    URL_MD5 ${Protobuf_md5}
+    ${COMMON_EP_ARGS}
+    PATCH_COMMAND ${CMAKE_COMMAND}
     ${Protobuf_PATCH_COMMAND}
-  BUILD_IN_SOURCE 1
-  CONFIGURE_COMMAND ./configure
+    BUILD_IN_SOURCE 1
+    CONFIGURE_COMMAND ./configure
     --prefix=${fletch_BUILD_INSTALL_PREFIX}
-  BUILD_COMMAND ${MAKE_EXECUTABLE}
-  INSTALL_COMMAND ${MAKE_EXECUTABLE} install
-)
+    BUILD_COMMAND ${MAKE_EXECUTABLE}
+    INSTALL_COMMAND ${MAKE_EXECUTABLE} install
+    )
+else()
+  # Build option for windows not yet generated
+  message( FATAL_ERROR "Protobuf 2 not yet supported on windows" )
+endif()
 
 fletch_external_project_force_install(PACKAGE Protobuf)
 
 set(Protobuf_ROOT ${fletch_BUILD_INSTALL_PREFIX} CACHE PATH "")
 
+if(NOT protobuf_BUILD_SHARED_LIBS)
+  if(WIN32)
+    set(PROTOBUF_LIBRARY "${Protobuf_ROOT}/lib/libprotobuf.lib")
+    set(PROTOBUF_LITE_LIBRARY "${Protobuf_ROOT}/lib/libprotobuf-lite.lib")
+    set(PROTOBUF_PROTOC_LIBRARY "${Protobuf_ROOT}/lib/libprotc.lib")
+  else()
+    set(PROTOBUF_LIBRARY "${Protobuf_ROOT}/lib/libprotobuf.a")
+    set(PROTOBUF_LITE_LIBRARY "${Protobuf_ROOT}/lib/libprotobuf-lite.a")
+    set(PROTOBUF_PROTOC_LIBRARY "${Protobuf_ROOT}/lib/libprotc.a")
+  endif()
+else()
+  if(WIN32)
+    set(PROTOBUF_LIBRARY "${Protobuf_ROOT}/lib/libprotobuf.lib")
+    set(PROTOBUF_LITE_LIBRARY "${Protobuf_ROOT}/lib/libprotobuf-lite.lib")
+    set(PROTOBUF_PROTOC_LIBRARY "${Protobuf_ROOT}/lib/libprotc.lib")
+  else()
+    set(PROTOBUF_LIBRARY "${Protobuf_ROOT}/lib/libprotobuf.so")
+    set(PROTOBUF_LITE_LIBRARY "${Protobuf_ROOT}/lib/libprotobuf-lite.so")
+    set(PROTOBUF_PROTOC_LIBRARY "${Protobuf_ROOT}/lib/libprotc.so")
+  endif()
+endif()
+
 file(APPEND ${fletch_CONFIG_INPUT} "
 #######################################
 # Google Protobuf
 #######################################
 set(Protobuf_ROOT \${fletch_ROOT})
+set(PROTOBUF_LIBRARY  \${PROTOBUF_LIBRARY})
+set(PROTOBUF_LITE_LIBRARY  \${PROTOBUF_LITE_LIBRARY})
+set(PROTOBUF_PROTOC_LIBRARY  \${PROTOBUF_PROTOC_LIBRARY})
 ")
 
diff --git a/CMake/fletch-tarballs.cmake b/CMake/fletch-tarballs.cmake
index 92da2bb1..8dd34b13 100644
--- a/CMake/fletch-tarballs.cmake
+++ b/CMake/fletch-tarballs.cmake
@@ -490,25 +490,22 @@ if(NOT WIN32)
 endif()
 
 # Protobuf
-if(NOT WIN32)
-  if (fletch_ENABLE_Protobuf OR fletch_ENABLE_ALL_PACKAGES OR AUTO_ENABLE_CAFFE_DEPENDENCY)
-    set(Protobuf_SELECT_VERSION "2.5.0" CACHE STRING "Select the  version of ProtoBuf to build.")
-    set_property(CACHE Protobuf_SELECT_VERSION PROPERTY STRINGS "2.5.0" "3.4.1")
-  endif()
-
-  set(Protobuf_version ${Protobuf_SELECT_VERSION})
+# WIN32 only supports the CMake version, 3.9.0
+if (WIN32)
+  set(Protobuf_SELECT_VERSION "3.9.0" CACHE STRING "Select the  version of ProtoBuf to build.")
+else()
+  set(Protobuf_SELECT_VERSION "3.9.0" CACHE STRING "Select the  version of ProtoBuf to build.")
+  set_property(CACHE Protobuf_SELECT_VERSION PROPERTY STRINGS "2.5.0" "3.9.0")
+endif()
 
-  if (Protobuf_version VERSION_EQUAL 2.5.0)
-    set(Protobuf_url "https://github.com/google/protobuf/releases/download/v${Protobuf_version}/protobuf-${Protobuf_version}.tar.bz2" )
-    set(Protobuf_md5 "a72001a9067a4c2c4e0e836d0f92ece4" )
-  elseif (Protobuf_version VERSION_EQUAL 3.4.1)
-    set(Protobuf_url "https://github.com/google/protobuf/releases/download/v${Protobuf_version}/protobuf-cpp-${Protobuf_version}.tar.gz" )
-    set(Protobuf_md5 "74446d310ce79cf20bab3ffd0e8f8f8f" )
-  elseif(Protobuf_version)
-    message(ERROR "Protobuf Version ${Protobuf_version} Not Supported")
-  endif()
-  list(APPEND fletch_external_sources Protobuf )
+if (Protobuf_SELECT_VERSION VERSION_EQUAL 2.5.0)
+  set(Protobuf_url "https://github.com/google/protobuf/releases/download/v${Protobuf_SELECT_VERSION}/protobuf-${Protobuf_SELECT_VERSION}.tar.bz2" )
+  set(Protobuf_md5 "a72001a9067a4c2c4e0e836d0f92ece4" )
+elseif (Protobuf_SELECT_VERSION VERSION_EQUAL 3.9.0)
+  set(Protobuf_url "https://github.com/protocolbuffers/protobuf/releases/download/v${Protobuf_SELECT_VERSION}/protobuf-all-${Protobuf_SELECT_VERSION}.zip")
+  set(Protobuf_md5 "4f042c8b46823a69db3dcbc7381b73f4" )
 endif()
+list(APPEND fletch_external_sources Protobuf )
 
 # Caffe
 set(InternalCaffe True)