Ya, I just did that with a cotyledon seedling about 1" tall...the other ones are still semi-hooks and it needed room. Normally, I don't transplant until first true leaves..but needed to in this case since one was so strong compared to the others.
So, I did up a 3" quare container w/ my pro-mix/perlite and a mild dose of 5-3-4 Terracycle granular fert. Seedling really seem to like the worm poop.
Pre-watered the soil..don't want to drown the baby, eh?
Made sure existing seedling's soil was nice and damp then used the end of plant marker to dig down around and just loosen it so I could pull/scoop it out, then just used the same stake to make a hole in the new container's dirt, and plopped it in leaving about 1/4" unburied.
Gave a tap down to secure it and a sprinkle of water, and 'tis all good.
Took about 3 mins to do.
PIX:
The original seed cup with remaining sprouts; one a hook, one just starting to unfold. Also the marker I used and the new transplant.
The chopped-down cup is gonna still have plastic wrap held on with a rubber band until the other two unfold at least.
Transplant closeup..one cotyledon tip was a bit tweaked when it came up stuck and I had to do surgery, but no worries. It'll be happier now and I won't have to worry about it.
I guess it helps I have smaller fingers and good dexterity. But just be gentle and careful...ya should be fine.
-QS