You can do it via metaprogramming; a functor can be converted to a list [name, param1, param2, ...], and then you can write normal Prolog operations on the list that bind variables and such, and then convert back. This page shows how to use that to build a higher-order map function: http://en.wikibooks.org/wiki/Prolog/Higher_Order_Programming

Here's a paper on other approaches; I'm not sure if any of the higher-order Prolog approaches ever caught on, though: http://www.cs.umbc.edu/courses/771/papers/mu_96_02.pdf