Ive found an adaption online as cap is a bit too wild for me as the box is open ended and i just want to cap the hole ive made. I create a big surface square off to the side and use orient3pt to place it over the 3 intesections followed by trim and use the box as a cutting object thus capping just the hole.
Or Pascals method of making a surface rectangular plane from the 3 intersections with a sphere and using boolean difference to cap works quite well, works when stepped through manually on extruded surfaces so I hope he can iron out the glitch because its ideal