diff --git a/list_for_Zhinan_for_SPECFEM2D_PMLs.txt b/doc/notes_about_CPML/list_for_Zhinan_for_SPECFEM2D_PMLs.txt
similarity index 100%
rename from list_for_Zhinan_for_SPECFEM2D_PMLs.txt
rename to doc/notes_about_CPML/list_for_Zhinan_for_SPECFEM2D_PMLs.txt
diff --git a/Carl_Tape_his_comments_on_the_adjoint_tomography_workflow_dec2014.txt b/doc/notes_about_tomography/Carl_Tape_his_comments_on_the_adjoint_tomography_workflow_dec2014.txt
similarity index 100%
rename from Carl_Tape_his_comments_on_the_adjoint_tomography_workflow_dec2014.txt
rename to doc/notes_about_tomography/Carl_Tape_his_comments_on_the_adjoint_tomography_workflow_dec2014.txt
diff --git a/Daniel_Peter_his_comments_on_the_current_adjoint_tomography_workflow_dec2014.txt b/doc/notes_about_tomography/Daniel_Peter_his_comments_on_the_current_adjoint_tomography_workflow_dec2014.txt
similarity index 100%
rename from Daniel_Peter_his_comments_on_the_current_adjoint_tomography_workflow_dec2014.txt
rename to doc/notes_about_tomography/Daniel_Peter_his_comments_on_the_current_adjoint_tomography_workflow_dec2014.txt
diff --git a/for_ADJOINT_TOMOGRAPHY_TOOLS_see_in_directory_utils_in_the_SPECFEM3D_package.txt b/utils/for_ADJOINT_TOMOGRAPHY_TOOLS_see_in_directory_utils_in_the_SPECFEM3D_package.txt
similarity index 100%
rename from for_ADJOINT_TOMOGRAPHY_TOOLS_see_in_directory_utils_in_the_SPECFEM3D_package.txt
rename to utils/for_ADJOINT_TOMOGRAPHY_TOOLS_see_in_directory_utils_in_the_SPECFEM3D_package.txt
diff --git a/replace_use_mpi_with_include_mpif_dot_h.pl b/utils/replace_use_mpi_with_include_mpif_dot_h.pl
similarity index 95%
rename from replace_use_mpi_with_include_mpif_dot_h.pl
rename to utils/replace_use_mpi_with_include_mpif_dot_h.pl
index 97f1dcc31..d88f807c7 100755
--- a/replace_use_mpi_with_include_mpif_dot_h.pl
+++ b/utils/replace_use_mpi_with_include_mpif_dot_h.pl
@@ -12,7 +12,7 @@
 # first clean trailing white spaces in all f90 files in the src/ sub-directories
 #
 
-      @objects = `ls src/*/*.f90 src/*/*.F90`;
+      @objects = `ls ../src/*/*.f90 ../src/*/*.F90`;
 
       foreach $name (@objects) {
             chop $name;
@@ -43,7 +43,7 @@
 # then perform the replacement in all f90 and F90 files in the src/ sub-directories
 #
 
-      @objects = `ls src/*/*.f90 src/*/*.F90`;
+      @objects = `ls ../src/*/*.f90 ../src/*/*.F90`;
 
       foreach $name (@objects) {
             chop $name;