You need to get the sprouts off the coffee filter before the tiny roots get too well established within the fibers of the coffee filter. If they've already grown into the filter, cut the filter with scissors instead of trying to rip the roots out of it.
If the roots aren't too long, I just poke a hole in the damp potting medium. Make sure the joint where the root meets the stem is level with or a fraction below the surface after you've firmed the potting medium. Add a little medium around the stem if the joint is above the surface after you've watered it in, so that the top part of the root doesn't dry out.
If the roots are too long or if I have to cut the filter, I make a steep downward-sloping trench instead of a straight hole. You can also just lay the roots on the surface and cover them if that's easier.
Be careful not to leave the roots exposed to the air any longer then necessary. It only takes about 30 seconds of exposure to the air for a young sprout's root tips to dry out beyond recovery. The sprout could still survive but it's a setback that you don't need. I also water them in as I go instead of waiting until I've planted them all.
The sprouts do need to go under lights immediately, otherwise they will start to stretch out in search of light. Temperature for growing seedlings does not need to be as warm as for germination so you don't need a heat mat for them. Room temperature is fine. Good air circulation will help to grow sturdy stems and avoid damping off.
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