I would like to know if there is any tool for migrating from ARM mcu's to Atmel? can any one help me on this topic?
I do not know Altium at all, but which specific part are you talking about ?
If I was in your shoes, I'd first of all contact the manufacturer of that part and ask if they had an Alitum version of it.
If you got no replies, I'd ask Altium's tech support (or a forum there).
If the part simply does not exist, I would create it myself.
As written above, I don't know anything about Alitum or creating parts in it, but all the parts I've used in my own PCB layout program, I've created myself, and it might be quicker to create a missing part than searching for it.
Be advised, though: You will need to be very careful and make sure you get all measurements correct.
If the part you're searching for is an IC, such as LQFP, QFN, BGA or similar, then use a generic footprint and create your specific part from that.