Secondary electrons from the substrate are picked up with a set of four scintillators on light-pipes on photomultiplier tubes. These are just like the detectors in scanning electron microscopes, except that there is no bias drawing in the scattered electrons. A bias would distort the writing field. Unfortunately the lack of bias makes the detectors inefficient, and so the system does not make a good electron microscope. Of course, it operates at 100kV, so that would make a terrible SEM in any case! It might surprise you to find that things easily seen in a SEM can be nearly invisible in the EBPG. That’s why the choice of materials for alignment marks is so critical and restricted.
Other e-beam writing systems use silicon diodes as detectors. These are not as fast as photomultiplier tubes, but they are more efficient at collecting the signal.