diff --git a/developer-doc/Makefile b/developer-doc/Makefile
index f7f25d33434476a76587254517d0e996e7cc86fd..aa8cbd94ee38c16f3a04eb829006fc6aef4e05c8 100644
--- a/developer-doc/Makefile
+++ b/developer-doc/Makefile
@@ -17,4 +17,12 @@ clean:
 
 coverage:
 	lcov -c -d ../src/ --output-file coverage.info
+# remove system headers:
+	lcov -r coverage.info "/opt/*" "/usr/*" -o coverage-tmp.info && mv coverage-tmp.info coverage.info
+# remove internal blas:
+	lcov -r coverage.info "*/blas/*.cpp" "*/blas/*.h" -o coverage-tmp.info && mv coverage-tmp.info coverage.info
+# remove internal lapack:
+	lcov -r coverage.info "*/lapack/*.cpp" "*/lapack/*.h" -o coverage-tmp.info && mv coverage-tmp.info coverage.info
+# remove internal molfile:
+	lcov -r coverage.info "*/molfile/*.cpp" "*/molfile/*.h" -o coverage-tmp.info && mv coverage-tmp.info coverage.info
 	genhtml -o coverage -t "plumed test coverage" coverage.info