Methods and systems for investigating a sample using a dual beam bifocal charged particle microscope, according to the present disclosure include emitting a plurality of charged particles toward the sample, forming the plurality of charged particles into a first charged particle beam and a second charged particle beam, and modifying the focal properties of at least one of the first charged particle beam and the second charged particle beam. The focal properties of at least one of the first charged particle beam and the second charged particle beam is modified such that the corresponding focal planes of the first charged particle beam and the second charged particle beam are different.