Kind of a controversial question but I am probably one of the few on this board who has actually replaced a common rail gasket so I'll go ahead and speak...
You can use some Scotch brite or some fine steel wool to get the grime off.
Just remember not to take too much time in one spot or you'll create a low spot and potential for future sealing problems.
Rememeber not to contaminate the oil pressure holes that are coming up out of the block. This could lead to a potential failure. Remove all debris when done cleaning.
When done I always rub down the cylinder walls with some oil to ease a dry startup and also clean up the block head surface with alcohol.
Remember you need to prep the head surface on the head itself also.
Its ok to have the lines left over from the old gasket. Just make sure to get any actual old gasket material cleared away.