I’m not sure how Refine landmark feature works, but you can register two volumes using thin-plate spline registration from two sets of landmarks using SlicerIGT extension’s Fiducial Registration Wizard module.
Fiducial points are stored in a csv file (using fcsv extension) in the following format:
# Markups fiducial file version = 4.10
# CoordinateSystem = 0
# columns = id,x,y,z,ow,ox,oy,oz,vis,sel,lock,label,desc,associatedNodeID
id can be any string unique within the file.