The data being filtered do not have to be functions of time. They can be functions of anything, so long as the sampling interval of the independent variable is constant. The frequency of the Fourier transformed data will then by cycles/unit, whatever that unit happens to be. If it is seconds, then cycles/second, or Hz, however if it millimetres, the frequency will be cycles/mm.
That aside, use the imfilter (or filter2) function to do the filtering, and perhaps the fspecial or similar functions to design the filter, if a more sophisticated filter is necesary.
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