The fabrication of nanometer size structures and complex devices for microelectronics is of increasing importance so as to meet the challenges of large-scale commercial applications. Soft lithography typically employs elastomeric polydimethylsiloxane (PDMS) molds to replicate micro- and nanoscale features. However, the difficulties of PDMS for nanoscale fabrication include inherent incompatibility with organic liquids and the production of a residual scum or flash layer that link features where the nano-structures meet the substrate. An emerging technologically advanced technique known as Pattern Replication in Non-wetting Templates (PRINT) avoids both of these dilemmas by utilizing photocurable perfluorinated polyether (PFPE) rather than PDMS as the elastomeric molding material. PFPE is a liquid at room temperature that exhibits low modulus and high gas permeability when cured. The highly fluorinated PFPE material allows for resistance to swelling by organic liquids and very low surface energies, thereby preventing flash layer formation and ease of separation of PFPE molds from the substrates. These enhanced characteristics enable easy removal of the stamp from the molded material, thereby minimizing damage to the nanoscale features. Herein we describe that PRINT can be operated in two different modes depending on whether the objects to be molded are to be removed and harvested (i.e. to make shape specific organic particles) or whether scum free objects are desired which are adhered onto the substrate (i.e. for scum free pattern generation using imprint lithography). The former can be achieved using a non-reactive, low surface energy substrate (PRINT: Particle Replication in Non-wetting Templates) and the latter can be achieved using a reactive, low surface energy substrate (PRINT: Pattern Replication in Non-wetting Templates). We show that the PRINT technology can been used to fabricate nano-particle arrays covalently bound to a glass substrate with no scum layer. The nanometer size arrays were fabricated using a PFPE mold and a self-assembled monolayer (SAM) fluorinated glass substrate that was also functionalized with free-radically reactive SAM methacrylate moieties. The molded polymeric materials were covalently bound to the glass substrate through thermal curing with the methacrylate groups to permit three dimensional array fabrication. The low surface energies of the PFPE mold and fluorinated glass substrate allowed for no flash layer formation, permitting well resolved structures.