How to reverse engineer a schematic from a circuit board

Step 7 Remove ground-planes

For the purposes of a schematic diagram, there is not much difference between ground-planes and the substrate.  Since you marked the free holes and ground-plane holes you can also remove these.

Note that if you are dealing with a 4 layer board, the internal layers are likely to be ground plane and power plane.  Any through plated holes which do not connect to anything you can see are likely to be connected to a power plane, however, this is no way guaranteed to be the case, as there may be other traces hidden away in there.  Hopefully you will be able to work this out at the end with the aid of a continuity tester.

Use the fuzzy select tool to select each ground plane area. You can also fuzzy de-select, fuzzy add-selection and fuzzy intersect-selection.  If fuzzy select is too uneven, use the circle, rectangle and  free selection tools.  It's easiest to use the free selection tool by creating a series of straight lines by clicking and moving.  When you click the first spot again, it will close the selection.  Before then, you can click and move any of the points you selected already.  You can also draw freehand with it, though I find this too uneven.  Grow the selection by one or two pixels (more if you have wide gaps between the tracks) to ensure there are no missed bits  - this will also clean up the edges a bit (Select > Grow) and save the selection to a channel in case you need it again (for example, if you have to start over).  Make sure you don't pinch out any bits of track, though.  Press delete to clear the selection.

Repeat for each ground plane area and the free holes, until they are all clear.