There are at least 2 different schools here and both seem to work quite well as you will see.
I prefer to straighten the cane first then I re-heat the nodes and roll them on a hard smooth surface with a block of hardwood. This compresses the nodes to almost the diameter of the internode.
Others straighten their cane then sand the nodes smooth. Because you are removing the rind you should seal these cane shafts. Unsanded cane has it's own built in sealer.
Note that in both cases the canes were straightened first then the nodes were dealt with. The node is the weal link in a cane arrow. If the sand first and try to straighten later the cane will generally break at a node.
If the nodes are not too pronounced you don't have to do anything with them. Once drawn a properly spined arrow shouldn't touch the bow when released so a slightly pronounced node shouldn't effect the arrows flight. I have a few river cane arrows that Mechslasher gave me. The nodes are very proud and as the arrows are drawn they make noise on the side of the bow. Once released I never hear a sound.