A flexible rail machine tool couples temporarily to a structure by vacuum cups and positions a tool head at any desired point over an area. The tool head can perform operations such as drilling, bolt insertion, and acquisition of dimension data. The flexible rail can conform to surface curvature in one or more axes. Tool head perpendicularity to the structure can be sensed and adjusted as needed. The as-attached position of the rail may be compensated for through coordinate transformation, allowing holes, for example, to be placed with substantial precision.