It depends a lot on the particular system to be used. Some systems are designed for relatively "large" samples (but we're not talking about bricks, here - perhaps you could scan a sample with height < 2cm, diameter laterally of 5cm ). These are typically "top down" AFM models, i.e. the entire microscope sits on top of the sample. This allows for larger samples.
In these cases, it depends on the specifics of the "sample holder". Usually, such microscopes can even scan WITHOUT the sample holder, though, so you are almost unlimited in sample size. Do remember though, that the sample must be flat. (Hence, no bricks!).

Sample-scanning microscopes (such as the Veeco multimode) are designed for small samples, will limit the sample size even more. Remember, AFM is a very high resolution technique, and is not really appropriate for very big samples. Also, it typically only scans very small areas (less than 100 micrometers x 100 micrometers usually), so there's little point in having a very big sample.