diff --git a/CMakeLists.txt b/CMakeLists.txt
index c5a3e96f42343649c90a9bd5889ca4b03d978616..d9251974b8dd47987cf7101639f8be8d8093e561 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -1,46 +1,66 @@
 cmake_minimum_required( VERSION 2.8 )
 
+# Explicitly add INCREMENTAL linking option to command lines.
+# http://www.cmake.org/pipermail/cmake/2010-February/035174.html
+set( MSVC_INCREMENTAL_DEFAULT ON )
+
+# ---------------------------------------------------------------------
+project( Elastix )
+
 # Include SuperElastix CMake scripts
-list( APPEND CMAKE_MODULE_PATH 
-  "${CMAKE_CURRENT_SOURCE_DIR}/CMake"
+list( APPEND CMAKE_MODULE_PATH
+  "${CMAKE_CURRENT_SOURCE_DIR}/CMake" 
 )
 
-if( CMAKE_HOST_WIN32 )
+if( ${CMAKE_CXX_COMPILER_ID} STREQUAL "MSVC" )
   include( elxWinConfig.cmake )
 endif()
 
-#---------------------------------------------------------------------
-project( Elastix )
-
-#---------------------------------------------------------------------
+# ---------------------------------------------------------------------
 # ITK
 
 find_package( ITK REQUIRED )
-set( ITK_NO_IO_FACTORY_REGISTER_MANAGER 1 )
 include( ${ITK_USE_FILE} )
 include( "${CMAKE_CURRENT_SOURCE_DIR}/CMake/elxITKRequiredModules.cmake" )
 
-#---------------------------------------------------------------------
+# ---------------------------------------------------------------------
 # Build Elastix
 
-#---------------------------------------------------------------------
-# Testing
+set( ELASTIX_COMMON_INCLUDE_DIRECTORIES
+  ${CMAKE_SOURCE_DIR}/Modules/Core/Common/include
+)
 
-# Build tests by default
-option( ELASTIX_BUILD_TESTING "Enable building tests." ON )
+set( ELASTIX_CORE_INCLUDE_DIRECTORIES
+  ${CMAKE_SOURCE_DIR}/Modules/Core/Blueprints/include
+)
+
+set( ELASTIX_INCLUDE_DIRECTORIES
+  ${ELASTIX_COMMON_INCLUDE_DIRECTORIES}
+  ${ELASTIX_CORE_INCLUDE_DIRECTORIES}
+)
+
+include_directories( ${ELASTIX_INCLUDE_DIRECTORIES} )
+add_subdirectory( Modules )
 
-# ExternalData module requires newer CMake versions
+# ---------------------------------------------------------------------
+# Testing
+
+# Testing requires CMake version 2.8.11 to download test data
 if( CMAKE_VERSION VERSION_LESS 2.8.11 )
-  set( ELASTIX_BUILD_TESTING OFF FORCE )
-  message( STATUS "ELASTIX_BUILD_TESTING was set to OFF because CMake version is less than 2.8.11")
+  set( ELASTIX_BUILD_TESTING_DEFAULT OFF )
+  message( STATUS "ELASTIX_BUILD_TESTING is set to OFF by default because CMake version is less than 2.8.11" )
+else()
+  set( ELASTIX BUILD_TESTING_DEFAULT ON )
 endif()
 
+option( ELASTIX_BUILD_TESTING "Enable building tests." ${ELASTIX_BUILD_TESTING_DEFAULT} )
+
 if( ELASTIX_BUILD_TESTING )
   enable_testing()
   add_subdirectory( Testing )
 endif()
 
-#---------------------------------------------------------------------
+# ---------------------------------------------------------------------
 # Build Documentation
 
 mark_as_advanced( ELASTIX_BUILD_DOXYGEN )
diff --git a/Modules/CMakeLists.txt b/Modules/CMakeLists.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ed8ac28d118442a7668ad4b7d36363991a040500
--- /dev/null
+++ b/Modules/CMakeLists.txt
@@ -0,0 +1,3 @@
+add_subdirectory(
+  Core
+)
\ No newline at end of file
diff --git a/Modules/Core/CMakeLists.txt b/Modules/Core/CMakeLists.txt
new file mode 100644
index 0000000000000000000000000000000000000000..dac4f7215cdf262d7f6c95cbbf835032a65bd4ce
--- /dev/null
+++ b/Modules/Core/CMakeLists.txt
@@ -0,0 +1,4 @@
+add_subdirectory(
+  Common
+  Blueprints
+)
\ No newline at end of file
diff --git a/Modules/Core/Common/CMakeLists.txt b/Modules/Core/Common/CMakeLists.txt
new file mode 100644
index 0000000000000000000000000000000000000000..fc2d9b4b5d0a3c36a784b891478afd95cc7c4302
--- /dev/null
+++ b/Modules/Core/Common/CMakeLists.txt
@@ -0,0 +1 @@
+include_directories( include )
\ No newline at end of file
diff --git a/Modules/Core/Common/include/elxMacro.h b/Modules/Core/Common/include/elxMacro.h
new file mode 100644
index 0000000000000000000000000000000000000000..d176d1a5dce073af5baa7421e4e35628bbfc9504
--- /dev/null
+++ b/Modules/Core/Common/include/elxMacro.h
@@ -0,0 +1,15 @@
+#ifndef __elxMacro_h
+#define __elxMacro_h
+
+/**
+ * Register class with the object factory and provide 
+ * associated RTTI (Run-Time Type Information)
+ */
+#define elxNewMacro( className, superClassName )        \
+  typedef className                       Self;         \
+  typedef itk::SmartPointer< Self >       Pointer;      \
+  typedef itk::SmartPointer< const Self > ConstPointer; \
+  itkNewMacro( Self );                                  \
+  itkTypeMacro( Self, superClassName );                 \
+
+#endif // __elxMacro_h
\ No newline at end of file
diff --git a/Testing/Unit/elxDataDirectories.h.in b/Testing/Unit/elxDataDirectories.h.in
index 835845d15b56febeb9f8d8ca19b81b8a344555b3..2081964057c33d7647da456782aff3e956135efd 100644
--- a/Testing/Unit/elxDataDirectories.h.in
+++ b/Testing/Unit/elxDataDirectories.h.in
@@ -1,5 +1,5 @@
-#ifndef __elxTestDataDirectories_h
-#define __elxTestDataDirectories_h
+#ifndef __elxDataDirectories_h
+#define __elxDataDirectories_h
 
 #define ELASTIX_UNITTEST_INPUT_DATA_DIR "@ELASTIX_UNITTEST_INPUT_DATA_DIR@"
 #define ELASTIX_UNITTEST_OUTPUT_DATA_DIR "@ELASTIX_UNITTEST_OUTPUT_DATA_DIR@"
diff --git a/Testing/Unit/elxDataManager.cxx b/Testing/Unit/elxDataManager.cxx
index e9aa4e4afd6f58cc26420fdd947bfbc29817cae9..d8da329264412ee10f1c8b8e3763cd34efe82877 100644
--- a/Testing/Unit/elxDataManager.cxx
+++ b/Testing/Unit/elxDataManager.cxx
@@ -5,25 +5,25 @@
 
 std::string
 DataManager
-::GetInput( const std::string filename ) const 
+::GetInputFullPath( const std::string filename ) const 
 {
-  const std::string path = this->GetInputDirectory() + this->GetPathSeparator() + filename;
+  const std::string path = this->GetInputDirectory() + this->GetFolderSeparator() + filename;
   return path;
 }
 
 std::string
 DataManager
-::GetOutput( const std::string filename ) const
+::GetOutputFullPath( const std::string filename ) const
 {
-  const std::string path = this->GetOutputDirectory() + this->GetPathSeparator() + filename;
+  const std::string path = this->GetOutputDirectory() + this->GetFolderSeparator() + filename;
   return path;
 }
 
 std::string
 DataManager
-::GetBaseline( const std::string filename ) const
+::GetBaselineFullPath( const std::string filename ) const
 {
-  const std::string path = this->GetBaselineDirectory() + this->GetPathSeparator() + filename;
+  const std::string path = this->GetBaselineDirectory() + this->GetFolderSeparator() + filename;
   return path;
 }
 
diff --git a/Testing/Unit/elxDataManager.h b/Testing/Unit/elxDataManager.h
index 61d4dcade79545c7c85210f663d9ca07390e3f5c..fb826d0414c3d31c9be56b4e65011c2fe20fb3fe 100644
--- a/Testing/Unit/elxDataManager.h
+++ b/Testing/Unit/elxDataManager.h
@@ -3,15 +3,17 @@
 
 #include <string>
 
-#include "itkMacro.h"
-#include "itkProcessObject.h"
-
+#include "elxMacro.h"
+#include "itkObjectFactory.h"
+#include "itkLightObject.h"
 #include "elxDataDirectories.h"
 
-class DataManager
+class DataManager : public itk::LightObject
 {
 public:
 
+  elxNewMacro( DataManager, itk::LightObject );
+
   DataManager()
   {
     this->m_InputDirectory = ELASTIX_UNITTEST_INPUT_DATA_DIR;
@@ -20,12 +22,21 @@ public:
   }
 
   std::string GetInputDirectory( void ) const { return this->m_InputDirectory; };
-  std::string GetOutputDirectory( void ) const { return this->m_InputDirectory; };
-  std::string GetBaselineDirectory( void ) const { return this->m_InputDirectory; };
+  std::string GetOutputDirectory( void ) const { return this->m_OutputDirectory; };
+  std::string GetBaselineDirectory( void ) const { return this->m_BaselineDirectory; };
 
-  std::string GetInput( const std::string filename ) const;
-  std::string GetOutput( const std::string filename ) const;
-  std::string GetBaseline( const std::string filename ) const;
+  std::string GetInputFullPath( const std::string filename ) const;
+  std::string GetOutputFullPath( const std::string filename ) const;
+  std::string GetBaselineFullPath( const std::string filename ) const;
+
+  std::string GetFolderSeparator() const
+  {
+#ifdef WIN32
+    return "\\";
+#else
+    return "/";
+#endif
+  } 
 
   std::string GetPathSeparator () const
   {