A simple and novel method for fabricating nanoporous-structure-coated silicon nitride tips for dip-pen nanolithography (DPN) by using the layer-by-layer (LbL) technique has been developed. The pore sizes can be adjusted by treating the LbL films coated onto the amino-terminated self-assembled monolayer (NH2-SAM)-functionalized AFM tip surface with a base solution for different periods of time. This hydrophilic porous material can absorb biomolecules easily and also provides a larger-volume ink reservoir compared with a bare silicon nitride tip. Proof-of-concept of the porous AFM tip is demonstrated by using fluorescent proteins as ink molecules to fabricate protein patterns at the micrometer and submicrometer length scales.