'flex' is the GNU update to 'lex'. In most general cases, either will do. 'lex' often refers to the original AT&T release.
'flex' (as well as lex) is a tool used to build "lexical analyzers" or "token parsers". Unless either of these terms really gets you excited, you really don't need to know more about them. (I happen to like building interpreters so f/lex, along with yacc/bison, are fun toys to play with!)
What you do need to know is that you can download them, install them and be on your way.
I will assume (based on the fact that you said "./configure") that you are operating on a Linux system. With this in mind, you should be able to find a nice RPM or even source for flex around and install it.
I will stop here to see if you need any further help on this...
--daveo