Is it permissible to suspend a living room by columns above two old graves, with three meters of air separating them from the room's floor, or must the two graves be moved to the village cemetery?

The Prophet, peace and blessings be upon him, forbade building over graves, whether it be a dome or a house. If the site of the two graves is a waqf (endowment), then what has been built over them must be demolished. However, if it is not a waqf, then demolition is not obligatory, but you have done wrong by this action. Exhumation is not permissible except out of necessity, and your situation is not one of necessity. If the graves are old and have decayed and turned into dust, then there is no harm in utilizing the land for building or planting, so long as it was not a waqf.