The way my heatsink was manufactured when I guaged it out with a flat steel guage it wasn't flat approaching the voltage regulators, it utilized the heatpipe technology and the end of the heatpipe was on the Voltage Regulators [V/R] side of the heatsink.
The heatpipe formed an upside down U and the vanes of the heatpipe towards the V/Rs were independent of the GPU contact plate, the bottom leg of the heatpipe was independent of the GPU plate except for about 3/16 of metal that was forged in the manufacturing process.
I carefully cut through that point allowing the bottom of the U configuration to move independently of the GPU contact plate, then scraped out enough of the heatsink over the V/Rs to allow the plate to seat on the RAM chips.
The V/Rs were holding the heatsink off the RAM chips between the V/Rs and the GPU contact plate, the cutting I did also allowed the contact plate to sit flat on the GPU, because without the cut tightening the screws cocked the GPU contact plate not allowing a flat contact with the GPU.
Some additional tweaking of the backplate required slight bending here and there to get it to sit perfectly flat on the RAM chips, using light, magnifying glass, and trial fits, using cheap thermal paste allowed me to get near perfect heatsink fits, which made all the difference in the stock heatsinks cooling capability.
Your heatsink may not be the same as mine, my cards are MSI NX7800GTX but the heatsink covered 80% of the entire card including the RAM chips on both sides of the cards, you may not have to cut the heatsink where I cut mine depending on how your heatsink is designed.
Carefully studying and examining your heatsink using light, will allow you to see everywhere it doesn't make good contact, it takes a lot of patience to achieve really good contact with all the contact points, but the end results are well worth the trouble.
Last Tip: After all my trial fittings with cheap thermal compound I wanted to extreme clean my cards and heatsinks before mounting everything for its final time.
I used a product you can pick up from the local Auto Parts Store, CRC QD Electronic Cleaner, its canned cleaner with a focusing nozzle, its flammable, and not too user friendly, use it outside the house and don't smoke while using it.
It will clean to factory cleaness in seconds removing every trace of old thermal compound, makes Rubbing Alcohol seem like cleaning with water, the cleaner chills the card and the outside air will form water droplets [The same thing happens with a glass of ICE water, water forms on the outside from the air condensation on the glass itself]looking like residue left behind, blow dry the cards and heatsinks with a hair dryer to ensure the water is gone.
The end result is perfectly clean cards and heatsinks with all residue gone.
Theres more than 1 brand of CRC cleaner, make sure you get the Electronic Cleaner, its designed not to hurt substrates and plastics!
If you undertake this project take your time and enjoy the process, I'm sure you'll be amazed as I was at how little contact the heatsink is actually making and what can be attained with the tweaking you can do to a stock cooler.