Is there a method to compute an average amplitude for 2D sinusoids using the F.C.'s?
Easy thing first: You might want to look into spatial statistics 


A fast library to compute Spatial Statistics in Matlab using FFTs.
A good description of Spatial Statistics from a past student


Long Stuff:

The trouble with comparing materials science information (eg AFM) is that the piece of material was measured at a position in space and time.  It is difficult to quantitatively compare images in one place and an image in another place.  

When you take the Fourier transform, you are measuring the frequency of that material at a position in space and time.  

You can remove the spatial dependency by taking a convolution of the Fourier transform with itself.  This process is akin to Point Distribution Functions, N-Point Statistics, or Joint Probability Density Functions.  The Spatial Statistics Matlab library can be applied to most image data.