The present disclosure pertains to our discovery of a particularly efficient method for etching a multi-part cavity in a substrate. The method provides for first etching a shaped opening, depositing a protective layer over at least a portion of the inner surface of the shaped opening, and then etching a shaped cavity directly beneath and in continuous communication with the shaped opening. The protective layer protects the etch profile of the shaped opening during etching of the shaped cavity, so that the shaped opening and the shaped cavity can be etched to have different shapes, if desired. In particular embodiments of the method of the invention, lateral etch barrier layers and/or implanted etch stops are also used to direct the etching process. The method of the invention can be applied to any application where it is necessary or desirable to provide a shaped opening and an underlying shaped cavity having varying shapes. The method is also useful whenever it is necessary to maintain tight control over the dimensions of the shaped opening.