Our limited understanding of the nervous system forms a bottleneck which impedes the effective treatment of neurological disorders. In order to improve patient outcomes it is highly desirable to interact with the nervous tissue at the resolution of individual cells. As neurons number in the billions and transmit signals electrically, high-density, cellular-resolution microelectrode arrays will be a useful tool for both treatment and research.This paper investigates the advantages and versatility of laser-patterning technologies for the development of such high-density microelectrode arrays in flexible polymer substrates. In particular, it aims to elucidate the mechanisms involved in laser patterning of thin polymers on top of thin metal layers. For this comparative study, a pulsed picosecond laser (Schmoll Picodrill) with two separate wavelengths (1064 nm (infrared (IR)) and 355 nm (ultraviolet (UV))) was used. A 5 $\mu$ m thick electroplated layer of gold (Au) was used to form the microelectrodes. Laser-patterning was investigated to expose the Au electrodes when encapsulated by two different thermoplastic polymers: thermoplastic polyurethane (TPU), and Parylene-C, with thicknesses of maximum 25 $\mu$ m. The electrode diameter and the distance between electrodes were reduced down to 35 $\mu$ m and 30 $\mu$ m, respectively. The structures were evaluated using optical microscopy and white light interferometry and the results indicated that both laser wavelengths can be successfully used to create high-density microelectrode arrays in polymer substrates. However, due to the lower absorption coefficient of metals in the IR spectrum, a higher uniformity of the exposed Au layer was observed when IR-based lasers were used. This paper provides more insight into the mechanisms involved in laser-patterning of thin film polymers and demonstrates that it can be a reliable and cost-effective method for the rapid prototyping of thin-film neural interfaces.