So I have an old FL250E bottom end that I want to use for a cr top end motor (( Internal Combustion Engine ? )). I was going to tear the case apart replace the seals, gasket and check the bearings.
Anyways I tried holding the case and hamering on the left hand of the crank like the manual says with no luck. I was just wondering if anyone had any tips on hard to split cases?
Thanks...

Sometimes they are real hard to split. Make sure and clean any rust off the crank snout so it can slide through the bearing, otherwise the bearing will come out of the case and still be stuck on the crank. Spray some PB Blaster down the oiling holes for the bearing as see if that might help loosen things up. The bearings can rust or seize into position on the crank making it difficult to separate the case. Use the biggest dead blow hammer you have and have someone you don't like hold the case. Swing real hard like a base ball bat and use curse words!

Thanks for the tip bill....
It is a pretty clean case... and there doesn't seem to be much rust on the crank, a little on the clutch side that i'll clean off with emmery cloth.
I' try soaking the bearings with WD-40 for a couple of days and try the big dead blow hammer like you said and hopeflly that does the trick.

The gasket holding the cases together is not what is giving you trouble. It is the bearing on the crank. The bearing is the hard part to get started moving. It will either have to have the crank slide through it, or the bearing will come out of the case still attached to the crank.

Once one side of the case comes off, support the other case half on a couple of wood blocks and tap the crank out of the other case 1/2. Honda never made a case puller for those engines, but I have seen home made versions. You could probably make one if you looked around the internet and copy what you see other Engine builders using. Take a look what they are using and see if you feel up to making one. I have always managed without one, so never built one for a 250 Engine.