Kolkovna has locations around the city and are in the upper mid range - quite decent Czech food:
http://www.kolkovna.cz
I highly recommend going to Pivovarsky Klub - some of the best beer in Prague. Nakladni Hermelin is quite good here (a traditional appetizer), and the mains are OK but nothing special. Oh and don't go to the second location they have - Pivovarsky Dum, just trust me that this one is much better
http://www.gastroinfo.cz/pivoklub/
If you know where in the city you are staying could probably give some other options as well - these two are both relatively central.