A poly(methyl methacrylate) assisted dry transfer method was developed to transfer graphene microflake onto a suspended SiN chip in an effective and efficient way for further graphene nanopore drilling for DNA analysis. Graphene microflakes can be patterned by e-beam lithography to a designed shape and size on a large scale of a few thousands simultaneously. Subsequently, individual graphene microflakes can be picked up and transferred to a target hole on a suspended SiN membrane with 1 µm precision via a site-specific transfer-printing method. Nanopores with different diameters from 3 to 20 nm were drilled on the as-transferred graphene membrane in a transmission electron microscope. This method offers a fast and controllable way to fabricate graphene nanopores for DNA analyses.