Open waveguides are widely used in modern photonic devices, such as microstructured fiber filters and sensors. Their absorption and transmission spectra are the most important properties in determining the overall performance of the photonic devices. The imaginary parts of their eigenvalues have been commonly used to calculate the absorption and consequently the transmission spectra. Here we show that this formulism is generally incorrect and not consistent with the simulation results obtained by the beam propagation method. We revisit the fundamental theory for the absorption of open waveguides and present a general formulism. We found that parity-time-symmetry transitions, which have been conventionally ignored, play a critical role in the properties of the coupled waveguide. The absorption and transmission are highly dependent on the physical length of the system. On the basis of our findings, optimization criteria for designing photonic sensors and filters are presented.