So, here's the recipe, resulting in the picture attached.
1. Start Builder
2. Add Si from Database (see below about Ge)
3. Builders>Surface (Cleave), let's cleave it 100 and leave all parameters at default
4. Bulk Tools>Repeat, 10x10x1
5. Rotate the view so you see the XY plane. Try to align it as well you can to be perpendicular to the screen plane.
6. Now, with the mouse, draw a rectangle to select, say, a square of 10x10 atoms (you have 20x20 now). It doesn't really matter where you start, but from the corner is of course easier to count.
7. Here's the trick now: press Ctrl+I to invert the selection; then press Delete to remove all atoms except those we selected in 6.
8. Center the system in all directions via Coordinate Tools>Center.
9. Hit the Passivate button
Now, this forms your basic structure, for which you can compute the band structure, or from which you can construct a device.
If you want Ge instead, since the passivator has a small problem with this, what you do is select Ge form the Database (to get the correct lattice constant) but then change all atoms to Si temporarily. Perform all steps above, and at the end (after passivation) change back to Ge. To select all atoms of a particular element, hold down Shift while double-clicking with the left mouse button on an atom. Then you can use the "Periodic Table" button to change all selected atoms to a new element.
