How to use MRPT libraries together with PCL?
1) Make sure you understand how CMake works and how you can create simple applications that #include and link correctly against MRPT.
2) Add the FIND_PACKAGE(PCL ...) command to your CMakeLists.txt file as usual. See this directory for working examples of MRPT-PCL integration in the same program.
Additionally, read this page for a list of classes and functions in MRPT which are prepared for interacting with PCL.