3D image sample frequency
2 mm period between samples is 500 samples per meter.  That's your sampling frequency.

Matlab's digital filter design functions (is that what you're using?) take a normalized frequency from 0 to 1, where 1 is the Nyquist frequency (1/2 the sampling frequency; the highest spatial frequency you can measure at that sample rate).

So if you wanted to filter at a spatial frequency of 100 cycles per meter (features that cycle every 1 cm), for instance, you would note that the Nyquist frequency is 250 cycles per meter, and enter a value of 100/250 = 0.4 for the normalized frequency.