We use a mixture of alcian blue/silver nitrate.
The alcian blue survives processing and is often helpful for
orientating specimens at the embedding stage (but of no use during
microscopy).
The silver nitrate marks the surgical margins and is useful during
microscopy (but not during embedding).
These comments apply not only to BCCs, for example, but also for
radical neck dissections.
We additionally use "Indian ink" to mark our Cut-up margins.
For example, the silver nitrate will indicate the "depth" of an
excision, the Indian ink the superior end of the specimen (for
example).
Russ Allison, Wales