How to make a deformed area planar/flat?

[system]

Hi.
I am making master molds of pieces of travertine stone, and right now i am using a Scanner to match the texture of samples given to me by the customer. I then machine the texture into a plastic type of material. The stones are flat to begin with but my scans are coming out deformed, i have deviation of upto about +/-1.00mm, which will not pass.

I realize it might be an issue with my scanner, I calibrate it regularily (almost every morning) but i still seem to have this problem. I dont really have time to investigate the cause.

Im fairly new at zbrush but i am using it to touch up the finish, as some of the details are lost in the scan. I am wondering if there is any way to select certain areas of my model and make them more planar. i would not like to flatten any
I use geomagic for processing the scans but i cant seem to find a way to flatten.

Any advice would be greatly appreciated. Thank you.

Here is a screen shot from geomagic with a plane for reference.

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[Spyndel]

Well, you can flatten a whole side easily with the clip curve brush. Make that your active selection brush by holding down shift-ctrl when clicking on the brush menu, then select clipcurv. Back in the canvas area, with Shift-Ctrl held down, draw out the clipping line where you want it, and zbrush will flatten to that line.

If you want a less absolute, more interactive flattening, try the Planar brush. The Planar brush will flatten down to the elevation where it first makes contact, or spackle in (flatten upwards) to that point if you hold down ALT while using it.