Self-organized InGaAs/GaAs quantum dots (QDs) stacked multilayers have been prepared by solid source molecular beam epitaxy. Cross-sectional transmission electron microscopy shows that the InGaAs QDs are nearly perfectly vertically aligned in the growth direction [100]. The filtering effect on the QDs distribution is found to be the dominant mechanism leading to vertical alignment and a highly uniform size distribution. Moreover, we observe a distinct infrared absorption from the sample in the range of 8.6–10.7 µm. This indicates the potential of QDs multilayer structure for use as infrared photodetector.