1. A method for determining a background signal intensity for a particular feature from a representation of scanned intensity values of a molecular array comprising data points and containing discrete features, each feature having a region of interest containing a number of data points, the method comprising: specifying a size for a background region corresponding to the feature; selecting as background data points those data points within the specified background region; filtering the selected data points to remove data points that lie within regions of interest of features of the molecular array near the feature; and determining the background signal intensity for the particular feature from the filtered, selected data points.