diff --git a/prism/src/dv/Makefile b/prism/src/dv/Makefile
index 84baba28..19906ce5 100644
--- a/prism/src/dv/Makefile
+++ b/prism/src/dv/Makefile
@@ -48,9 +48,15 @@ $(PRISM_DIR_REL)/$(CLASSES_DIR)/$(THIS_DIR)/%.class: %.java
 
 $(PRISM_DIR_REL)/$(INCLUDE_DIR)/DoubleVector.h: $(PRISM_DIR_REL)/$(CLASSES_DIR)/$(THIS_DIR)/DoubleVector.class
 	($(JAVAH) -classpath $(PRISM_DIR_REL)/$(CLASSES_DIR) -jni -o $@ $(THIS_DIR).DoubleVector; touch $@)
+	@if [ "$(LIBSUFFIX)" = ".dll" ]; then \
+	  (dos2unix $@) \
+	fi; 
 
 $(PRISM_DIR_REL)/$(INCLUDE_DIR)/IntegerVector.h: $(PRISM_DIR_REL)/$(CLASSES_DIR)/$(THIS_DIR)/IntegerVector.class
 	($(JAVAH) -classpath $(PRISM_DIR_REL)/$(CLASSES_DIR) -jni -o $@ $(THIS_DIR).IntegerVector; touch $@)
+	@if [ "$(LIBSUFFIX)" = ".dll" ]; then \
+	  (dos2unix $@) \
+	fi; 
 
 $(PRISM_DIR_REL)/$(LIB_DIR)/$(LIBPREFIX)dv$(LIBSUFFIX): $(O_FILES)
 	$(LD) $(SHARED) $(LDFLAGS) -o $@ $(O_FILES) $(LIBRARIES)
diff --git a/prism/src/hybrid/Makefile b/prism/src/hybrid/Makefile
index 9af46572..afe2b1e4 100644
--- a/prism/src/hybrid/Makefile
+++ b/prism/src/hybrid/Makefile
@@ -51,6 +51,9 @@ $(PRISM_DIR_REL)/$(CLASSES_DIR)/$(THIS_DIR)/%.class: %.java
 
 $(PRISM_DIR_REL)/$(INCLUDE_DIR)/PrismHybrid.h: $(PRISM_DIR_REL)/$(CLASSES_DIR)/$(THIS_DIR)/PrismHybrid.class
 	($(JAVAH) -classpath $(PRISM_DIR_REL)/$(CLASSES_DIR) -jni -o $@ $(THIS_DIR).PrismHybrid; touch $@)
+	@if [ "$(LIBSUFFIX)" = ".dll" ]; then \
+	  (dos2unix $@) \
+	fi; 
 
 $(PRISM_DIR_REL)/$(LIB_DIR)/$(LIBPREFIX)prismhybrid$(LIBSUFFIX): $(O_FILES)
 	$(LD) $(SHARED) $(LDFLAGS) -o $@ $(O_FILES) $(LIBRARIES)
diff --git a/prism/src/jdd/Makefile b/prism/src/jdd/Makefile
index 010dc94e..85e523e8 100644
--- a/prism/src/jdd/Makefile
+++ b/prism/src/jdd/Makefile
@@ -46,15 +46,27 @@ $(PRISM_DIR_REL)/$(CLASSES_DIR)/$(THIS_DIR)/%.class: %.java
 
 $(PRISM_DIR_REL)/$(INCLUDE_DIR)/JDD.h: $(PRISM_DIR_REL)/$(CLASSES_DIR)/$(THIS_DIR)/JDD.class
 	($(JAVAH) -classpath $(PRISM_DIR_REL)/$(CLASSES_DIR) -jni -o $@ $(THIS_DIR).JDD; touch $@)
+	@if [ "$(LIBSUFFIX)" = ".dll" ]; then \
+	  (dos2unix $@) \
+	fi; 
 
 $(PRISM_DIR_REL)/$(INCLUDE_DIR)/JDDNode.h: $(PRISM_DIR_REL)/$(CLASSES_DIR)/$(THIS_DIR)/JDDNode.class
 	($(JAVAH) -classpath $(PRISM_DIR_REL)/$(CLASSES_DIR) -jni -o $@ $(THIS_DIR).JDDNode; touch $@)
+	@if [ "$(LIBSUFFIX)" = ".dll" ]; then \
+	  (dos2unix $@) \
+	fi; 
 
 $(PRISM_DIR_REL)/$(INCLUDE_DIR)/JDDVars.h: $(PRISM_DIR_REL)/$(CLASSES_DIR)/$(THIS_DIR)/JDDVars.class
 	($(JAVAH) -classpath $(PRISM_DIR_REL)/$(CLASSES_DIR) -jni -o $@ $(THIS_DIR).JDDVars; touch $@)
+	@if [ "$(LIBSUFFIX)" = ".dll" ]; then \
+	  (dos2unix $@) \
+	fi; 
 
 $(PRISM_DIR_REL)/$(INCLUDE_DIR)/DebugJDD.h: $(PRISM_DIR_REL)/$(CLASSES_DIR)/$(THIS_DIR)/DebugJDD.class
 	($(JAVAH) -classpath $(PRISM_DIR_REL)/$(CLASSES_DIR) -jni -o $@ $(THIS_DIR).DebugJDD; touch $@)
+	@if [ "$(LIBSUFFIX)" = ".dll" ]; then \
+	  (dos2unix $@) \
+	fi; 
 
 $(PRISM_DIR_REL)/$(LIB_DIR)/$(LIBPREFIX)jdd$(LIBSUFFIX): $(O_FILES)
 	$(LD) $(SHARED) $(LDFLAGS) -o $@ $(O_FILES) $(LIBRARIES)
diff --git a/prism/src/mtbdd/Makefile b/prism/src/mtbdd/Makefile
index 306d7288..d08908b3 100644
--- a/prism/src/mtbdd/Makefile
+++ b/prism/src/mtbdd/Makefile
@@ -49,6 +49,9 @@ $(PRISM_DIR_REL)/$(CLASSES_DIR)/$(THIS_DIR)/%.class: %.java
 
 $(PRISM_DIR_REL)/$(INCLUDE_DIR)/PrismMTBDD.h: $(PRISM_DIR_REL)/$(CLASSES_DIR)/$(THIS_DIR)/PrismMTBDD.class
 	($(JAVAH) -classpath $(PRISM_DIR_REL)/$(CLASSES_DIR) -jni -o $@ $(THIS_DIR).PrismMTBDD; touch $@)
+	@if [ "$(LIBSUFFIX)" = ".dll" ]; then \
+	  (dos2unix $@) \
+	fi; 
 
 $(PRISM_DIR_REL)/$(LIB_DIR)/$(LIBPREFIX)prismmtbdd$(LIBSUFFIX): $(O_FILES)
 	$(LD) $(SHARED) $(LDFLAGS) -o $@ $(O_FILES) $(LIBRARIES)
diff --git a/prism/src/odd/Makefile b/prism/src/odd/Makefile
index 470bf3c1..7f209a82 100644
--- a/prism/src/odd/Makefile
+++ b/prism/src/odd/Makefile
@@ -46,6 +46,9 @@ $(PRISM_DIR_REL)/$(CLASSES_DIR)/$(THIS_DIR)/%.class: %.java
 
 $(PRISM_DIR_REL)/$(INCLUDE_DIR)/ODDUtils.h: $(PRISM_DIR_REL)/$(CLASSES_DIR)/$(THIS_DIR)/ODDUtils.class
 	($(JAVAH) -classpath $(PRISM_DIR_REL)/$(CLASSES_DIR) -jni -o $@ $(THIS_DIR).ODDUtils; touch $@)
+	@if [ "$(LIBSUFFIX)" = ".dll" ]; then \
+	  (dos2unix $@) \
+	fi; 
 
 $(PRISM_DIR_REL)/$(LIB_DIR)/$(LIBPREFIX)odd$(LIBSUFFIX): $(O_FILES)
 	$(LD) $(SHARED) $(LDFLAGS) -o $@ $(O_FILES) $(LIBRARIES)
diff --git a/prism/src/prism/Makefile b/prism/src/prism/Makefile
index 2e5d007b..f2e01b38 100644
--- a/prism/src/prism/Makefile
+++ b/prism/src/prism/Makefile
@@ -44,6 +44,9 @@ $(PRISM_DIR_REL)/$(CLASSES_DIR)/$(THIS_DIR)/%.class: %.java
 
 $(PRISM_DIR_REL)/$(INCLUDE_DIR)/PrismNative.h: $(PRISM_DIR_REL)/$(CLASSES_DIR)/$(THIS_DIR)/PrismNative.class
 	($(JAVAH) -classpath $(PRISM_DIR_REL)/$(CLASSES_DIR) -jni -o $@ $(THIS_DIR).PrismNative; touch $@)
+	@if [ "$(LIBSUFFIX)" = ".dll" ]; then \
+	  (dos2unix $@) \
+	fi; 
 
 $(PRISM_DIR_REL)/$(LIB_DIR)/$(LIBPREFIX)prism$(LIBSUFFIX): $(O_FILES)
 	$(LD) $(SHARED) $(LDFLAGS) -o $@ $(O_FILES) $(LIBRARIES)
diff --git a/prism/src/sparse/Makefile b/prism/src/sparse/Makefile
index b36bcecc..74a80805 100644
--- a/prism/src/sparse/Makefile
+++ b/prism/src/sparse/Makefile
@@ -52,6 +52,9 @@ $(PRISM_DIR_REL)/$(CLASSES_DIR)/$(THIS_DIR)/%.class: %.java
 
 $(PRISM_DIR_REL)/$(INCLUDE_DIR)/PrismSparse.h: $(PRISM_DIR_REL)/$(CLASSES_DIR)/$(THIS_DIR)/PrismSparse.class
 	($(JAVAH) -classpath $(PRISM_DIR_REL)/$(CLASSES_DIR) -jni -o $@ $(THIS_DIR).PrismSparse; touch $@)
+	@if [ "$(LIBSUFFIX)" = ".dll" ]; then \
+	  (dos2unix $@) \
+	fi; 
 
 $(PRISM_DIR_REL)/$(LIB_DIR)/$(LIBPREFIX)prismsparse$(LIBSUFFIX): $(O_FILES)
 	$(LD) $(SHARED) $(LDFLAGS) -o $@ $(O_FILES) $(LIBRARIES)