If I understand you right, then you can just flatten the image, select the part you don't want by whatever means, then delete the selection. The deleted section will be transparent and you can save it as a .psd or .png.

I think another problem may be that Poser doesn't appear to honour transparency either in the background image or when applied to an object. A workaround might be to create a transmap and instead of putting your background image into Poser's background, create an appopriately sized and positioned plane and apply the image to that, so the plane acts as a background. Then you can apply your transmap to the plane and mask off the part you don't want to to see.

Steve