Two circuit bearing substrates, such as a rigid electronic circuit board and a flexible circuit film, each having large arrays or multiple arrays of surface contact pads or traces, are mechanically and electrically joined without relocating the substrates during the bonding process by using a bonding apparatus with multiple working tools or bond shoes. The bonding apparatus includes a fixture for holding the circuit bearing substrates with a joining layer between them, and two or more independently operated heated bond shoes that compress different portions of the circuit bearing substrates with the joining layer, such as a layer of anisotropic conductive film.