When characterizing roughness from a metrological point of view, what is important is to determine the so-called "sampling length" and "evaluation length". From both of them are derived the number of sampling points and the measurement spacing. Both sampling and evaluation lengths were defined by international standards.
To answer more practically your question, check for these following links:
Here is an excerpt from http://cdn.intechopen.com/pdfs/33450.pdf :
"The numerical evaluation of roughness is always preceded by removal of waviness from the measured profile. This is achieved in a surface texture measuring instrument by using an analog or digital filter. In order to exclude waviness, a limiting wavelength has to be specified. This limiting wavelength is referred to as cutoff. The cutoff is given in mm or Inch and the following values are available in many instruments, 0.08, 0.25, 0.8, 2.5, and 8 nm. The cutoff selected must be short enough to exclude irrelevant long wavelength and at the same time long enough to ensure that enough texture has been included in the assessment to give meaningful results. Usually five cutoff settings are used for assessment, and overall traverse length is seven cutoffs".