I've always used Indian Ink. It shows every little crease and detail nicely and the colour stays true over a very long time. I've tried paint but it doesn't show the lines very clearly. A tip is to buy acid-free paper then it won't go yellow over time. All this stuff is available at art supply shops. Indian ink (artist quality ink) would be fairly safe... it's the stuff they use to fingerprint people... palm readers use it too. Personally I think there are more harmful chemicals in the average bottle of supermarket baby wash compared to using this as a "once off".
Speak to the hospital. They usually have inking pads for taking hand and foot prints (not always for the nicest of reasons but things like NICU babies etc ) They should be able to tell you where to get them from or may be able to get one for you in hospital. We access them from newborn care / NICU when we need one at work.
My little niece was in NICU and they used what looked like an ink pad to do her footprints. They had one that was all one colour, and another that was tri-coloured, so her toes were one colour, the middle of her foot another and her heel another one. You might be able to borrow it, or they should be able to tell you where to get one.
I used face paint for DD's feet and her footprints came up beautifully in my dearly departed FIL last bday card. 8 months on and the prints are still on the card as bright as they were the day I did them. It wiped off nicely too!
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