Power-based side channel attacks are a significant security risk, especially for embedded applications. To improve the security of such devices, protected logic styles have been proposed as an alternative to CMOS. However, they should only be used sparingly, since their area and power consumption are both significantly larger than for CMOS. We propose to augment a processor, realized in CMOS, with custom instruction set extensions, designed with security and performance as the primary objectives, that are realized in a protected logic. We have developed a design flow based on standard CAD tools that can automatically synthesize and place-and-route such hybrid designs. The flow is integrated into a simulation and evaluation environment to quantify the security achieved on a sound basis. Using MCML logic as a case study, we have explored different partitions of the PRESENT block cipher between protected and unprotected logic. This experiment illustrates the tradeoff between the typ...