If I uninstall the mod, will it delete the associated surfaces?

No, the associated surfaces will not be deleted automatically. Here's a console command that can delete the surfaces for you:

/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.

I see. I prefer to use Editor Extension then. There should be an API for this: Factorio to keep mod's uninstallation scripts and run it when mod has been removed. Thank you for your quick reply!