Processing of thin-walled parts with large dimensions in conditions of wide range production poses a number of technological problems. One of the most important among them is the provision of alignment on both sides of the hole who passing through the opposite walls of the part. Is essential the alignment of the spindles while processing of the hole , if used for this purpose machining center with two horizontal spindles . In the publication is presented research about possibilities to solve the problem by controlling of spindles alignment. For this purpose are carried out contact coordinate measurements of the hole in one spindle using 3D touch probe which is fixed in the other spindle.