The Non-contact (Optical) profilometer would be the best for very rough surface. Further how your sample is? You can also use contact profilometer with large radius tip for very rough surface.

In my opinion non-contact profilometers are any day better.

If your sample is rough and you want to avoid that in your measurement then go for a stylus with large radius.

Optical profilers are good. there are many optical profilers which come along with noise reduction ability.it is interesting to read about it.

may be you can look up for Dektak profilers for more detail