Structural studies done on HgSe nanoclusters fabricated in the pores of two types of zeolite frameworks, LTL (tubular pore) and Nd-Y (nearly spherical pore), are presented. Nanoclusters were synthesized in these zeolite frameworks via chemical vapor deposition. Anomalous X-ray scattering (AXS) studies were performed on both HgSe/zeolite-Y and HgSe/zeolite-L systems. As a result, we present two distinct structural models for NdY/HgSe and LTL/HgSe systems. A remarkable feature present in our X-ray diffraction (XRD) patterns, diffuse scattering, will also be discussed using our initial results of the atomic pair distribution function (PDF) studies. X-ray structural work is complemented using the results of optical and Raman studies.