- Import your STL model into blender
- Press Tab to enter vertex editing mode.
- Press Z to enter wireframe mode (if you aren't already)
- Press B to box select all the lowest points or the points you want to be the lowest.
- Press S to scale, Z to only effect the z-axis, and and type 0 (zero) to flatten the points to the same z plane.
- Press G and then Z to move the flat bottom to the apropaite z height. At this point it's okay to eyeball it since ReplicatorG will make sure the model is on the build platform.
- Press A to select all points and select the "Remove Doubles" button on the left side bar to do a little cleanup.
That's all there is so it. You get a nice flat bottom. You may still have some non-manifold points to clean up depending on the geometry that your flattening. You can either hunt for them manually by pressing ctrl+alt+M or just export and run it through netfabb one more time.
I've used this trick so many times