I'm using Ipi and Poser... I read in the Wiki that there is an issue with the hands. They mention using something to cut off the hands so that this does not effect the character.

Does anybody have experience with this and what is the workflow for that? I'm not sure what to do.

First, see if you have any issues with hands with your version of Poser. If not, then why bother?
If there are issues, then chopping the hands can be done after exporting BVH character from poser. Open BVH in bvhacker. In the tree view of joints, select the parent joint of right wrist (that should be right forearm), right click and choose Remove Descendants. Make the same with the left joints. Save changes. Then import the resulting BVH to Mocap Studio.
Of course, after chopping hands from the skeleton, you cannot transfer wrist/finger movements from Mocap Studio to your character.

Thanks for the tip... I'm using Poser Pro 2014... There is an issue, at least, with the hands. When I bring the character back in to poser and run the animation... The hands become deformed... They look like they have a bad case of arthritis.

So I was going to chop off the hands and see if this helps.

Hi Danakinobi, I use Daz characters when animating with the Ipi BVHs, and I knock out all of the hand keyframes in the Daz timeline, and manually apply these - http://www.daz3d.com/v4-hand-poses It says they're compatible with Poser. You could maybe give this a try?

Hope that helps!