Current and future emission levels on Particulate Matter (PM) will require diesel engines to use Diesel Particulate Filters (DPF). One of the challenges of using a DPF is the requirement to generate high temperature exhaust flow (typically 550 - 650 degrees C) to enable filter regeneration, especially at cold temperatures and transient conditions. Maintaining constant temperature and low emissions during regeneration presents a number of controls challenges. This is especially true for burner systems which have complex air, fuel, and ignition systems. This paper outlines the controls and diagnostics of a burner system. Details of the burner system component modeling, thermal modeling of combustion, combustion flame detection, and system control and diagnostics are also illustrated. Application data is presented to demonstrate performance and robustness of the system at different engine conditions.