Scrubs is filmed at a real life medical clinic. The clinic has been closed for years and the producers decided to use the building. Plus most of the items on the set were bought in by the cast.
NBC leased and refurbished the disused hospital for the program. The lower and upper floors of the hospital are used as other sets and production offices.
A lot of the cast bring their dogs to play on set. The floor above the one they film on is vacant. That is where the dogs hang out.