As per your response you are using windows project on Linux. The windows project template is different from Linux project template. So if you are building a windows project on Linux , the make file will have cs-rm instead of rm. In order to change the project settings, you may try replacing the .cproject and .project file with the same file from one of the FX3 Linux SDK example project. Once the files are replaced you may open the project in eclipse and build it. Please try the same and let us know your observation.
Thanks a lot! That seems to have done the trick.