Automatic background signal removal for input data, such as for spectrometry data, is provided. Input data includes input pixel points, such as those read by a CCD spectrometer or chromatography device, and intensity values corresponding to the data points. A distribution of changes in the intensity values between the data points is determined, and a noise level is judged by setting a threshold for the distribution. A noise region is identified as a predetermined number of consecutive input points for which the changes in the intensity values are within the noise level. Adjacent noise regions may be connected and the background signal is thus determined and subtracted. A spike noise region may also be identified and filtered, such that a peak obtained from fewer than a second predetermined number of the pixel points is determined as a spike, not a true peak. Non-spike large amplitude noises are optionally filtered.