For masking contact pads, there are two widely used solutions. Firstly, the application of a liquid peelable masking material, which can be either air/heat dried, or UV cured.
These materials are designed to peel easily from the contacts after coating, through the conformal coating layer, thus removing the coating from the keep-out area.
The second method is the use of a tape... polyester or Kapton tape are common, and the process is largely the same. Key thing to note, ensure the adhesive in the tape is non-silicone based, or else you may encounter dewetting and lack of coating adhesion.
For both methods, it is usually best to demask as soon as the coating is dry to the touch. The drier or more cured the coating, the harder it can be to remove the masking material through the coating and the more likely you are to damage the coating, requiring touch-up to give the desired cosmetic finish.
Depending upon the volumes of boards you have to coat, a selective robot may be a better long-term choice, thereby largely eliminating the need to mask.
Hope this helps.