Prilep's Institute and Museum is the useful indoor stop in town, especially if you want context before heading up to the fortress or out to the monasteries. Its collections cover archaeology, local history, and the wider Pelagonia region, rather than trying to be a grand national museum.
It is not the reason to come to Prilep, but it rounds out the visit well. Go when the weather is too hot for the hills, or when you want the town's long history explained in one place.