The effect of washing with acidic and basic solutions on the internal structure (fluctuations in the density and the size of the polymer clusters through the gel) of the imprinted and the random PNIPA (polyN-isopropylacrylamide) hydrogels has been studied by using steady-state fluorescence technique, swelling kinetics and SEM images. When the gel is imprinted, fluctuations in the density and the size of the polymer clusters decrease through the gel; i.e., the gel becomes more homogeneous. Washing with acid causes no considerable change in the internal structure of the both gels, but washing with base causes a drastic change in the structure by breaking the bonds between the polymer strands. The release rate of target molecules for the imprinted gel becomes considerably higher than for the random one regardless of the washing condition since the target molecules are trapped in the dense blobs of the random gel. The change in the internal structure of the gels upon washing is modeled by a spring approximation.