Fortunately, there is more than one way to explicitly flush the caches.
The instruction “wbinvd” writes back modified cache content and marks the caches empty. It executes a bus cycle to make external caches flush their data. Unfortunately, it is a privileged instruction. But if it is possible to run the test program under something like DOS, this is the way to go. This has the advantage of keeping the cache footprint of the “OS” very small.
Additionally, there is the “invd” instruction, which invalidates caches without flushing them back to main memory. This violates the coherency of main memory and cache, so you have to take care of that by yourself. Not really recommended.
For benchmarking purposes, the simplest solution is probably copying a large memory block to a region marked with WC (write combining) instead of WB. The memory mapped region of the graphics card is a good candidate, or you can mark a region as WC by yourself via the MTRR registers.
You can find some resources about benchmarking short routines at Test programs for measuring clock cycles and performance monitoring.