I've just responded to your other post about the ps3000aSetBandwidthFilter.
The main difference is that the Instrument Driver will require the use of different prototype and thunk files in conjunction with the Linux drivers. We will be providing support for 64-bit versions of MATLAB on Linux in due course.
You will also need to have downloaded the libps3000a and libpswrapper packages (see http://www.picotech.com/linux.html
If you e-mail in as requested in that post, we can provide the required files for you to run on Linux.
Are you using MATLAB 2014b?