Dear Drax,
A toughned glass modification is tough job.Try to cut it and it would braek off. Try grinding ,it would go up in splinters.The only way you can do that is to heat up the glass gradually by sticking to a heatup curve (which depends on the composition of the glass) anneal it following the annaeling curve of that glass and then do the modification. Once done you would have to re toughen the glass by following a heat up curve and then quenching of the glass.
Why not try and modify the holder of that glass portion.That is easier.
Regards
Chatterjee