hi, heres a software that does what u want. its free to use for 30days after which u have to purchase. im not sure if it saves in SEP although it does have plenty of formats. u will have to check if yr still on the hunt for software
Only information about sep-files I could find was on the link below.
It is associated with the Tagged Image File Format (TIFF).
So you would need a digitising program that would recognise the format (or have it converted to a bitmap or jpg first) and then digitise it.