diff --git a/Cantera/Makefile.am b/Cantera/Makefile.am
new file mode 100644
index 000000000..ae31608e3
--- /dev/null
+++ b/Cantera/Makefile.am
@@ -0,0 +1,20 @@
+# $Id: $
+
+# will need to add python and matlab 
+SUBDIRS                 = src
+
+h_sources               = cantera.h
+cc_sources              = cantera.cpp
+
+INCLUDES                = 
+AM_FCFLAGS              = $(INCLUDES)
+AM_CFLAGS               = $(INCLUDES)
+AM_CPPFLAGS             = $(INCLUDES) 
+
+lib_LTLIBRARIES         = libcantera.la
+library_includedir      = $(includedir)
+library_include_HEADERS = cantera.h
+libcantera_la_LDFLAGS   = $(all_libraries) -release $(GENERIC_RELEASE)
+libcantera_la_SOURCES   = $(cc_sources) $(h_sources)
+
+
diff --git a/Cantera/Makefile.in b/Cantera/Makefile.in
deleted file mode 100755
index 1d0500e66..000000000
--- a/Cantera/Makefile.in
+++ /dev/null
@@ -1,57 +0,0 @@
-#/bin/sh
-###############################################################
-#  $Author: hkmoffa $
-#  $Date: 2007/05/06 17:16:43 $
-#  $Revision: 1.8 $
-#
-#  Copyright 2001 California Institute of Technology
-#  See file License.txt for licensing information
-#
-###############################################################
-
-build_f90=@BUILD_F90@
-build_python=@BUILD_PYTHON@
-build_matlab = @BUILD_MATLAB@
-
-all:
-	cd src; @MAKE@
-	cd cxx; @MAKE@
-	cd clib/src; @MAKE@
-ifeq ($(build_f90),1)
-	cd fortran/src; @MAKE@
-endif
-	cd user; @MAKE@
-
-clean:
-	cd src;                            @MAKE@ clean
-	cd cxx;                            @MAKE@ clean
-	cd clib/src;      $(RM) .depends ; @MAKE@ clean
-	cd python;                         @MAKE@ clean
-ifeq ($(build_f90),1)
-	cd fortran/src;   $(RM) .depends ; @MAKE@ clean
-endif
-	cd user;          $(RM) .depends ; @MAKE@ clean
-
-depends:
-	cd src;         @MAKE@ depends
-	cd cxx/src;     @MAKE@ depends
-	cd clib/src;    @MAKE@ depends
-ifeq ($(build_f90),1)
-	cd fortran/src; @MAKE@ depends
-endif
-ifeq ($(build_matlab),1)
-	cd matlab;      @MAKE@ depends
-endif
-	cd user;        @MAKE@ depends
-
-install:
-	cd src; @MAKE@ install
-	cd cxx/src; @MAKE@ install
-	cd clib/src; @MAKE@ install
-ifeq ($(build_f90),1)
-	cd fortran/src; @MAKE@ install
-endif
-	cd user; @MAKE@ install
-
-# end of file
-
diff --git a/Cantera/src/Makefile.am b/Cantera/src/Makefile.am
new file mode 100644
index 000000000..713874f7d
--- /dev/null
+++ b/Cantera/src/Makefile.am
@@ -0,0 +1,7 @@
+# $Id: $
+
+# need to add CXX_INCLUDES
+# will need to add python and matlab 
+SUBDIRS                 = base converters equil kinetics numerics oneD spectra transport zeroD
+
+
diff --git a/Cantera/src/Makefile.in b/Cantera/src/Makefile.in
deleted file mode 100755
index 4408231f2..000000000
--- a/Cantera/src/Makefile.in
+++ /dev/null
@@ -1,48 +0,0 @@
-#/bin/sh
-###############################################################
-#  $Author: dggoodwin $
-#  $Date: 2007/12/15 17:15:50 $
-#  $Revision: 1.58 $
-#
-#  Copyright 2001 California Institute of Technology
-#
-###############################################################
-
-all:
-	cd base; @MAKE@ all
-	cd equil; @MAKE@ all
-	cd zeroD; @MAKE@ all
-	cd oneD;  @MAKE@ all
-	cd converters; @MAKE@ all
-	cd transport;  @MAKE@ all
-	cd thermo;     @MAKE@ all
-	cd kinetics;   @MAKE@ all
-	cd numerics;   @MAKE@ all
-	cd spectra;   @MAKE@ all
-
-clean:
-	cd base;       $(RM) .depends ; @MAKE@ clean
-	cd equil;      $(RM) .depends ; @MAKE@ clean
-	cd zeroD;      $(RM) .depends ; @MAKE@ clean
-	cd oneD;       $(RM) .depends ; @MAKE@ clean
-	cd converters; $(RM) .depends ; @MAKE@ clean
-	cd transport;  $(RM) .depends ; @MAKE@ clean
-	cd thermo;     $(RM) .depends ; @MAKE@ clean
-	cd kinetics;   $(RM) .depends ; @MAKE@ clean
-	cd numerics;   $(RM) .depends ; @MAKE@ clean
-	cd spectra;    $(RM) .depends ; @MAKE@ clean
-
-depends: 
-	cd base; @MAKE@ depends
-	cd equil; @MAKE@ depends
-	cd oneD; @MAKE@ depends
-	cd zeroD; @MAKE@ depends
-	cd converters; @MAKE@ depends
-	cd transport; @MAKE@ depends
-	cd thermo; @MAKE@ depends
-	cd kinetics; @MAKE@ depends
-	cd numerics; @MAKE@ depends
-	cd spectra; @MAKE@ depends
-
-TAGS: 
-	etags *.h *.cpp
diff --git a/configure.ac b/configure.ac
index 97420855f..3dbd36240 100644
--- a/configure.ac
+++ b/configure.ac
@@ -55,7 +55,7 @@ AM_SANITY_CHECK
 # DX_INIT_DOXYGEN(cantera, doxygen/cantera.dox, docs) 
 
 # Generate Output Files
-AC_OUTPUT( Makefile Cantera/Makefile test_problems/Makefile examples/Makefile doxygen/Makefile)
+AC_OUTPUT( Makefile Cantera/Makefile test_problems/Makefile examples/Makefile) #doxygen/Makefile
 
 # FINAL SUMMARY
 AX_SUMMARIZE_CONFIG