This paper describes a case study and design flow of a secure embedded system called ThumbPod, which uses cryptographic and biometric signal processing acceleration. It presents the concept of HW/SW acceleration transparency, a systematic method to accelerate Java functions in both software and hardware. An example of acceleration transparency for a Rijndael encryption function is presented. The embedded prototype hardware platform is also described. Acceleration transparency yields software and hardware performance gains of 333X. Categories and Subject Descriptors E5 [Case Studies]; E3 [HW/SW Co-Design]: specification, modeling, co-simulation and performance analysis, system-level scheduling and partitioning. General Terms Performance, Design, Experimentation.