We report the effect of dissimilar anion anneals on the properties of layered quantum dot structures exhibiting vertical self-organization. Such anneals may provide an additional means of controlling dot properties, such as composition, size, and position. In addition, the modification of surface strain is critical to the subsequent nucleation of dots after the initial seed layer. Anion exchange may modify the strain at the semiconductor surface. We find that the effects Of P-2 and As-4 anneals on InAs quantum dot size distributions are different. P-2 anneals at relatively high temperatures (350 degreesC) can cause the loss of the three-dimensional morphology due to surface exchange. P-2 anneals at lower temperatures (300 degreesC) appear to improve the uniformity of the dot size distribution. This behavior is not observed for anneals under AS(4). The dot size uniformity decreases by annealing dots under AS(4) at 300 degreesC.