Yes you can, just do these simple steps
First you write a parser to read the location.cfg to find the map's file name via Map::GetProtoId
Then you write a parser to read the map.fomap
Then you use your favourite Map::GetItem of choice and delete everything
Do that for critters too
Remember that fomap you parsed? Well time to place some critters and items back on the map yo.
If a script is attached to the fomap and you want to run that again, Map::SetScript that shit
Optionally Map::SetData 0 to 99 to whatever default value you choose or not at all!
Or you can try Map::Reload