An intermediate structure for a microfluidic device and a method for manufacturing a microfluidic device are provided. The method includes: a) providing a first substrate having a first layer thereon, and a second layer on the first layer; b) forming a first nanopore in the second layer, in such a way that a part of the first layer coincides with a bottom of the first nanopore; c) exposing said part of the first layer to a liquid etchant, thereby forming a cavity under the first nanopore, the cavity having a larger width than a width of the bottom of the first nanopore; d) filling the first nanopore and the cavity with a filling material, thereby forming a first plug; e) forming a bottom fluidic access for the nanopore by removing part of the first substrate and part of the first layer so as to expose the plug; and f) removing the plug, thereby fluidly connecting the bottom fluidic access to the nanopore.