Usually people would use WorldEdit and simply //cut the land before pasting or building the spawn on top of the newly formed flat land. Also when inputting a schematic it can sometimes leave flat areas around the edges determined by how the schematic was created in the first place. Very few people, I believe, would take the time to manually dig out the flat land area when they could easily do it with a few quick commands through WorldEdit.
Might wanna take a look at the WorldEdit plugin for minecraft. I assume you are running a server, in which case it's a simple as dropping the worldedit.jar into your plugins folder. Then you should take a look at a tutorial on basic usage like the one below. Worldedit is also available as a client side modification for your local worlds. Simply put, you use the 'wand' or a wooden axe to select a region to operate on, then use commands such as '//set item' and '//cut' to carve out a flat space on your map.
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