A method for bonding and interconnecting a first IC device arranged on a first substrate to a second IC device arranged on a second substrate, wherein each IC device comprises a dielectric bonding layer (5a,5b) at its outer surface, and wherein each IC device further comprises one or more metal contact structures (4a, 4b), the method comprising the consecutive steps of: • positioning the first substrate with respect to the second substrate, with the bonding layers of the first and second IC device facing each other, by aligning a first metal contact structure in the first IC device to a second metal contact structure in the second IC device, • direct bonding of the substrates, thereby forming a substrate assembly, • optionally thinning the first substrate, • producing by a lithography step and an etching procedure, a first opening (16,30) in the first substrate, until reaching said first metal contact structure, wherein said first metal contact structure partially covers a cross-section of the first opening (16,30), • with the first metal contact structure acting as a mask, etching one or more second openings (16',30') in the second substrate, stopping on said second metal contact structure, the first and second opening thereby forming an aggregate opening (16+16';30+30'), • producing an isolation layer on the sidewalls and the bottom of at least the first opening (16,30), • removing the isolation layer from at least the bottom of the first opening, while essentially maintaining the isolation layer on at least the sidewalls of the first opening, without applying a lithography step, • producing a metal contact plug in the aggregate opening, said metal plug interconnecting the first and second contact structures (4a,4b). characterized in that the step of removing the isolation layer is performed by a plasma treatment comprising the steps of: • introducing the assembly in a plasma atmosphere comprising one or more polymer-forming components and one or more etching components, • treating the assembly by inducing a plasma such that a protective polymer layer is formed on at least portions of the isolation layer present on the upper surface of the assembly and on at least portions of the isolation layer present on upper portions of the sidewalls of the first opening (16,30), thereby protecting the portions of the isolation layer where the protective polymer layer is being formed, from the plasma, wherein portions of the isolating layer being exposed to the plasma are etched. • positioning the first substrate with respect to the second substrate, with the bonding layers of the first and second IC device facing each other, by aligning a first metal contact structure in the first IC device to a second metal contact structure in the second IC device, • direct bonding of the substrates, thereby forming a substrate assembly, • optionally thinning the first substrate, • producing by a lithography step and an etching procedure, a first opening (16,30) in the first substrate, until reaching said first metal contact structure, wherein said first metal contact structure partially covers a cross-section of the first opening (16,30), • with the first metal contact structure acting as a mask, etching one or more second openings (16',30') in the second substrate, stopping on said second metal contact structure, the first and second opening thereby forming an aggregate opening (16+16';30+30'), • producing an isolation layer on the sidewalls and the bottom of at least the first opening (16,30), • removing the isolation layer from at least the bottom of the first opening, while essentially maintaining the isolation layer on at least the sidewalls of the first opening, without applying a lithography step, • producing a metal contact plug in the aggregate opening, said metal plug interconnecting the first and second contact structures (4a,4b). • introducing the assembly in a plasma atmosphere comprising one or more polymer-forming components and one or more etching components, • treating the assembly by inducing a plasma such that a protective polymer layer is formed on at least portions of the isolation layer present on the upper surface of the assembly and on at least portions of the isolation layer present on upper portions of the sidewalls of the first opening (16,30), thereby protecting the portions of the isolation layer where the protective polymer layer is being formed, from the plasma, wherein portions of the isolating layer being exposed to the plasma are etched.