Combustion process was studied from the injection until the late combustion phase in an high swirl optically accessible combustion bowl connected to a single cylinder 2-stroke high pressure common rail compression ignition engine. Commercial diesel and blends of diesel and n-butanol (20%: BU20 and 40%: BU40) were used for the experiments. A pilot plus main injection strategy was investigated fixing the injection pressure and fuel mass injected per stroke. Two main injection timings and different pilot-main dwell times were explored achieving for any strategy a mixing controlled combustion. Advancing the main injection start, an increase in net engine working cycle (>40%) together with a strong smoke number decrease (>80%) and NOx concentration increase (@50%) were measured for all pilot injection timings. Compared to diesel fuel, butanol induced a decrease in soot emission and an increase in net engine working area when butanol ratio increased in the blend. A noticeable increase in NOx was detected at the exhaust for BU40 with a slight effect of the dwell-time. Spectroscopic investigations confirmed the delayed auto-ignition (~60 ms) of the pilot injection for BU40 compared to diesel. The spectral features for the different fuels were comparable at the start of combustion process, but they evolved in different ways. Broadband signal caused by soot emission, was lower for BU40 than diesel. Different balance of the bands at 309 and 282 nm, due to different OH transitions, were detected between the two fuels. The ratio of these intensities was used to follow flame temperature evolution.