If you want to avoid cluttering of the source with object files use the build directory to generate your object files. To do that do it as follows. Copy the axisconfigure file from c directory to c/build directory. Next just change the following line of it ./configure --libdir=/home/damitha/projects/axiscpp/c/release into ../configure --libdir=/home/damitha/projects/axiscpp/c/release Now from c/build directory run sh axisconfigure