Once you have quantitated your data SeqMonk offers a variety of different types of filter to reduce your initial set of probes down to a small subset of regions of interest.
All filters operate on the currently active probe list (the one you have selected in the Data View), and they will produce a subset of the current active list.
It is worth spending some time looking through the different filters available. You should also remember that it can be very useful to requantitate your data to allow you to filter against another property of your data, and that this will not affect your current probe lists as long as you only change the quantiation and do not rerun the probe generation step.