This research involves the development of a novel method to produce micro-embossed features with an aspect ratio of three and negligible flash on polymer surfaces. An embossing technique that utilizes localized heating (ultrasonic energy) was used with polystyrene and polypropylene substrates. It was demonstrated that when foamed substrates were used, the amount of flash produced was negligible compared to non-foamed substrates, which has been a significant unresolved problem with embossing using localized heating. The depth of micro-embossed features as a function of heating times and amplitudes of ultrasonic embossing is detailed in this paper, along with a characterization of complex embossed geometries. It was seen that embossing depth was generally proportional to heating time and amplitude until the maximum feature depth was achieved. We have also demonstrated this technology for embossing of micro-features for lab-on-a-CD applications.