diff --git a/SuperBuild/CMake/External_fftw.cmake b/SuperBuild/CMake/External_fftw.cmake
index 424447955b361caa9503465a5d5c025afcc7694e..2bddeafce9268bb0a92a0b9fde8a089c83e59f63 100644
--- a/SuperBuild/CMake/External_fftw.cmake
+++ b/SuperBuild/CMake/External_fftw.cmake
@@ -24,6 +24,8 @@ SETUP_SUPERBUILD(FFTW)
 
 set(FFTWF_SB_SRC ${CMAKE_BINARY_DIR}/FFTW/src/FFTWF)
 set(FFTWD_SB_SRC ${CMAKE_BINARY_DIR}/FFTW/src/FFTWD)
+set(FFTWF_SB_BUILD ${CMAKE_BINARY_DIR}/FFTW/build/FFTWF)
+set(FFTWD_SB_BUILD ${CMAKE_BINARY_DIR}/FFTW/build/FFTWD)
 
 # Compile the float version of FFTW
 ExternalProject_Add(FFTWF
@@ -31,7 +33,7 @@ ExternalProject_Add(FFTWF
   URL "http://www.fftw.org/fftw-3.3.8.tar.gz"
   URL_MD5 8aac833c943d8e90d51b697b27d4384d
   SOURCE_DIR ${FFTWF_SB_SRC}
-  BINARY_DIR ${FFTWF_SB_SRC}
+  BINARY_DIR ${FFTWF_SB_BUILD}
   INSTALL_DIR ${SB_INSTALL_PREFIX}
   DOWNLOAD_DIR ${DOWNLOAD_LOCATION}
   CMAKE_CACHE_ARGS
@@ -57,7 +59,7 @@ ExternalProject_Add(FFTWD
   URL "http://www.fftw.org/fftw-3.3.8.tar.gz"
   URL_MD5 8aac833c943d8e90d51b697b27d4384d
   SOURCE_DIR ${FFTWD_SB_SRC}
-  BINARY_DIR ${FFTWD_SB_SRC}
+  BINARY_DIR ${FFTWD_SB_BUILD}
   INSTALL_DIR ${SB_INSTALL_PREFIX}
   DOWNLOAD_DIR ${DOWNLOAD_LOCATION}
   CMAKE_CACHE_ARGS