Your best bet might be to remove the table top and see if the frame is out of square or just wasn't installed properly. Just buttering down 3/4 MDF and hoping it will fix your problem is just asking for more problems. Using a lot of pressure to flatten down a piece of MDF just might crack the MDF.

You say it is not flat but you don't say exactly what is wrong. Is it twisted? Is it bowing up or down in the middle? Is it in the shape of a bowl?