Individual factory interior surfaces are all managed by the mod and there is currently no support for removing them while the mod is installed. Uninstalling the mod is also not recommended, this would break every single factory building.
To remove all Factorissimo content at once from your save, you could uninstall the mod, remove all surfaces with the following command, then reinstall the mod.
/c for n,s in pairs(game.surfaces) do if string.sub(n,1,14) == 'Factory floor ' then game.delete_surface(n) game.player.print("Deleted surface '"..n.."'") end end
Be sure to only run this command after uninstalling the mod.