what those guys up there said.
Here's a pic for reference. The fuel filter sits inside the fuel pump assy. You're gonna hafta loosen up the fuel rail, remove the feeder hose (from the pump assy to the fuel rail), disconnect the vacuum hose, remove the brackets and then you'll be able to remove the fuel pump.
After that (yup), you're gonna need to disassemble the fuel pump assembly. 4 screws, later, your pump assembly should be in two pieces. Be careful taking it apart, though...you don't wanna damage anything inside.
The actual pump itself sits in the lower part of the assembly. Since it's out and everything, you may as well clean the feeder and return line screens. It's gonna be one HECKUVA job to get it out, but with some patience it'll come right out.
The upper part of the assembly is where the fuel filter sits. Some people recommend putting an external filter in, as the stock filters are junk.
To remove the fuel filter, you're gonna need to pry that cap off. Be mindful of that little placement/fitment peg. And you may also want to get some O-rings as well, as you'll need to replace the two o-rings that go around the assemblies.
Also be mindful of the spring holding the filter in place. You really don't wanna lose that.
If worse comes to worse, shoot me a PM. I've had trouble with the fuel pump and assembly, so I've acquired a good deal of information about it. My bike's a 99, BTW.
Best of luck and don't hesitate to shoot me a PM.