You can implement p+ shunting, pn junction, and isolating guard rings, or isolating shields made of n-type buried layer surrounded by deep trench (isolated p-wells), but I don't think any of these will completely eliminate the substrate noise.
You may consider implementing additional circuit level compensation in your PLL. It was a paper presented at DesignCon this year about active cancellation of substrate noise coupling with a VCO example, which you can find and download for free at
http://www.noisecoupling.com Regards,
ci