In this paper, we describe a novel and simple process for the fabrication of all-transparent and encapsulated polymeric nanofluidic devices using nano-indentation lithography. First, a nanomechanical probe is used to 'scratch' nanoscale channels on polymethylmethacrylate (PMMA) substrates with sufficiently high hardness. Next, polydimethylsiloxane (PDMS) is used twice to duplicate the nanochannels onto PDMS substrates from the 'nano-scratched' PMMA substrates. A number of experiments are conducted to explore the relationships between the nano-indentation parameters and the nanochannel dimensions and to control the aspect ratio of the fabricated nanochannels. In addition, traditional photolithography combined with soft lithography is employed to fabricate microchannels on another PDMS 'cap' substrate. After manually aligning the substrates, all uncovered channels on two separate PDMS substrates are bonded to achieve a sealed and transparent nanofluidic device, which makes the dimensional transition from microscale to nanoscale feasible. The smallest dimensions of the achievable nanochannels that we have demonstrated thus far are of ~20 nm depth and ~800 nm width, with lengths extendable beyond 100 μm. Fluid flow experiments are performed to verify the reliability of the device. Two types of colloidal solution are used to visualize the fluid flow through the nanochannels, that is, ethanol is mixed with gold colloid or fluorescent dye (fluorescein isothiocyanate), and the flow rate and filling time of liquid in the nanochannels are estimated based on time-lapsed image data. The simplicity of the fabrication process, bio-compatibility of the polymer substrates, and optical transparency of the nanochannels for flow visualization are key characteristics of this approach that will be very useful for nanofluidic and biomolecular research applications in the future.