Feature Matching is one of the central issues of model-based recognition and an important component of most object recognition systems. The feature matching technique can be applied in image alignment, 3D secure reconstruction, motion tracking, object recognition and in pharmacophore based molecular alignment. Even though numerous algorithms exist for feature recognition and search yet the efficiency of these have considerable room for improvement. This has necessitated a continuous search for better performing algorithms. The combination of geometric hashing technique and tolerance limits for a given set of known interactions can be used for the pharmacophore modelling based search. The algorithm proposed is precise as compared with the previous existing algorithms. This algorithm is better in its runtime complexity.