The short answer is: no, you can’t pre-select the networks you wish to scan. During your survey, all networks in range are included in the scan.
The reason for this is that pre-selecting APs would actually make your survey take longer, because Netspot would need to make multiple calls to the AirPort interface, instead of just one.
Once your survey is complete, you can easily select only the networks you are interested in from the list of networks on the left-hand sidebar. Only the selected networks will be shown in the heat map visualizations. You can also filter out weaker APs by adjusting the AP detection proximity setting.
NetSpot PRO also make it easy to group networks by specific criteria, add hidden APs, and to pre-select specific APs for active scanning.