Pleasemesh,
Have you seen this paper: http://www.comsol.com/academic/papers/628/ it may help you.
You can also try asking on the http://www.comsol.com/community where you may get a faster answer.
Have you seen this paper yet on Confinement Loss Computations in Photonic Crystal Fibres using a Novel Perfectly Matched Layer Design? http://www.comsol.com/papers/1083/
It may help.
Jacob,
Have you tried asking this question in the COMSOL Community forum?
http://www.comsol.com/community/
You may get a fast answer.
Brian Kenyon
COMSOL - Web Program Manager
Have you tried asking your question in the COMSOL Community Discussion Forum?
Your question may get answered faster there. http://www.comsol.com/community