While holes can be filled, there is a good chance they show up for a reason, and it is a sign of quality issues with your inputs. One potential issue could be the illumination difference among your two images. You may want to examine just how similar your L.tif
and R.tif are (in stereo_gui). Then, I will suggest using --stereo-algorithm asp_mgm, if that's not what you are using. Then, if you are using ASP 3.1.0, the latest, you may want to search for the convergence angle value in your stereo_pprc log file (in the
output directory). If that is too small, say under 5 degrees, it can cause issues.
Lastly, if you really want to fill the holes, note in point2dem the option --dem-hole-fill-len. You can also use --search-radius-factor 2 (or 3) to fill things a bit more. But these would be cosmetic fixes. If your inputs are good, normally the DEM comes out
quite filled and seamless. In a produced DEM the tool dem_mosaic can fill holes as well.