Most of the book should work fine. In fact, the 3.5 changes to how monsters receive feats and skills makes the system a bit easier to use. Around March of this year, I'll have time to work up a document on how to create monsters using the 3.5 rules and the MHB. Now that monsters progress like characters, it's a lot easier to determine a monster's CR simple by giving it X HD for its monster type, then using the system to give it special abilities. Under 3.0, monster feats and skill ranks were really driven by stats and other outside factors that made it hard to regularly predict where creatures would fall into CR categories based solely on HD.
The tricky thing is that there isn't a linear relationship between base HD and CR. For example, a 1 HD magical beast might be CR 1, but a vanilla 5 HD magical beast might be CR 3 before you add any abilities.
In most cases, even the templates should remain the same. I've done some 3.5 update work specifically to learn the differences between the two versions, and it looks like the biggest changes are that monsters receive a lot more skill ranks and about 1 bonus feat.