I've transformed my matrix into reflection seismic data format and loaded it into processing software. There is a tool, that performs a f-k transformation and plots a f-k diagram. In this diagram You can mark an area in the f-K domain by mouse click which should be filtered out. The result of this filtering is plotted in another window.
I think it should be possible too to generate a tool like this in Matlab .... but of cause it will be some work. So it was much more comfortable to change data format.