A fluidic control chip was incorporated to control delivery of PCR cocktail to a multi-well (MW) continuous flow PCR (CFPCR) chip. Passive micro-assembly was implemented for modular integration of the fluidic control chip and the CFPCR chip using three sets of passive alignment structures to obtain exact kinematic constraint. The fluidic control chip was assembled with the CFPCR chip by thermal bonding and used for parallel amplification of DNA fragments. Successful, simultaneous amplification of DNA fragments, with lengths of 99bp, 125bp, 150bp, 200bp, 500bp, 997bp, was demonstrated on the whole, high throughput CFPCR platform with a distributed thermal system.