Disk I/O times vary widely due to a large variety of factors including rotational speed, location on the disk, fragmentation, etc. Accessing a file twice in a very short time will usually result in the second access completing significantly faster then the first. For these reasons, you should not include I/O speed in any formal bencharking tests.
Are you expecting to measure performance externally, by insturmentation, or using local time accumulators? If you're doing it externally, you're pretty much screwed. If you're using insturmentation, then the post-processor program should be able to provide you with a per-method breakdown, so you can simply eliminate those methods that do I/O (assuming you've structured the code to do that). If you're using a local accumulators, simply place the calls to the time functions around the major blocks you're interested in and have the program print out the total accumulator(s) at the end.