A microfluidic chip includes microfluidic channels, elements for thermally and optically isolating the microfluidic channels, and elements for enhancing the detection of optical signal emitted from the microfluidic channels. The thermal and optical isolation elements may comprise barrier channels interposed between adjacently-arranged pairs of microfluidic channels for preventing thermal and optical cross-talk between the adjacent microfluidic channels. The isolation element may alternatively comprise reflective film embedded in the microfluidic chip between the adjacent microfluidic channels. The signal enhancement elements comprise structures disposed adjacent to the microfluidic channels that reflect light passing through or emitted from the microfluidic channel in a direction toward a detector. The structures may comprise channels or a faceted surface that redirects the light by total internal reflection or reflective film material embedded in the microfluidic chip.