Provided are devices and methods for polymer analysis, in which labeled polymers are translocated along nanochannels that have illuminated detection regions within. As a labeled polymer translocates along the nanochannel and the labels pass over the illuminated detection regions, the labels become detectable (e.g., where different labels fluoresce in response to different wavelengths present at different illumination regions), and the user generates a spatial map of the location of the various labels along the length of the polymer. The location of the labels is then correlated to one or more structural characteristics of the polymer.