I've tried putting bees and comb into frames - - and it didn't work very
well.  The comb simply never got 'attached' to the frames.  The only
difference was my bees had moved into a seldom used shed and built from the
rafters.  We had combs that exteded downward for THREE FEET!!
 
I would suggest, after you have the hive isolated that you stand that section
on the ground.  Place a piece of plywood with a large hole in the center on
top of that section - and a regular hive body on top of the log/plywood.  The
bees will 'move up' into the hive body, eventually vacating the log.  At this
point the log can be disposed of.  Keep building on top of the body.
 
My $.02 worth.