I found this site when dealing with ways to create custom LEGO pieces.
I use Bentley's Microstation V8i ss2 to do my Modeling
I have had 2 models printed as prototypes so far but I haven't been 100% successful.
After a little bit of trial and error in Microstation I am able to create models that are printable. My first model I had a conversion issue. The issue that I am currently having is whether the printed items are the same size as I modeled them or if I have the correct sizes for LEGO pieces. (I need to get a micrometer) The last piece I recieved is a little bit smaller than I expected. A minifig can hold it but the connection is loose.
Microstation... I still have nightmares about rendering with that lol. Never used it for modeling. If you want to check the size use either Netfabb basic, or Meshlab (both free) to check your dimensions. I know there are a few Lego heads around here that may be able to help you more on that side.The Mad Moder