Colloidal self-assembly is an efficient method to obtain ordered 3D nanostructures. However, it suffers from the drawback that defects are difficult to eliminate in the self-assembled nanostructures. In this report, a method to reduce the defect density is proposed. It has been observed earlier that during self-assembly, the colloidal system goes through a transition state with a higher mobility than the final rigid nanostructure. This offers an opportunity to anneal out defects like vacancies and dislocations. Using in-situ reflectance spectra measurements of a self-assembling system, we demonstrate the feasibility of this transition state annealing method. (c) 2007 Elsevier B.V. All rights reserved.