As analysis systems shrink in size to microfluidic scales and devices, there is a need to improve temperature control in the microscale for temperature-sensitive processes. Technology that combines accurate temperature measurement and 3D spatial control of the temperature distribution is limited by common 2D layer-based microfluidic fabrication techniques but can be realized with 3D printed microfluidic chips. This work presents an iterative process to create a microfluidic chip using multi-material 3D printing to improve temperature sensing and create an even temperature around a target volume. Through an iterative process, verification is presented of fluorophore viability (specifically CdTe quantum dots) after being secured in place by cured PR48 3D printing resin, thus confirming the possibility of fluorescent thermometry as an accurate non-contact temperature sensing method. Numerical analyses of various geometries of chip design iterations are also presented verifying spatially even heating due to the placement of heating sources in the microfluidic chip. Combining the fluorescent thermometry and improved heating will lead to improved temperature control in microfluidic devices.