Virtually all emeralds are "treated" - i.e. fracture filled in some
way. It could be with a natural oil, could be Canada balsam, could be
an epoxy resin. I'd guess you heated the stone enough to carbonize
that filling. If that is the case, you now have organic gunk baked
black in the pores and fissures of the stone, comparable to the
baked buildup in the domestic oven and similarly difficult to remove.
Fortunately the stone itself is pretty much immune to reagents. If
my diagnosis is correct I would first of all coat the stone with
"Easy-Off" or similar oven cleaner overnight. See what that does. If
this does not help (always assuming my diagnosis of burnt organic
fracture filling is in fact the correct one) you may have to proceed
to sterner stuff like boiling the stone in concentrated nitric acid.
If it gets to that stage and if the stone is valuable enough to
justify such a "rescue" I'd have this done by an expert. Hot nitric
acid - and similar aggressive reagents - should not messed with.
Once the residue has been dissolved out the stone will need to be
re-treated, again, a specialized process. Above all do not put the
stone in the ultrasonic. Most emeralds are flawed and fissured,
hence the prevalence of fracture filling. Ultrasonic may cause cracks
that went partway through the stone to go the rest of the distance,
leaving you with two stones instead of one, or worse. Been there