Heritage structures are important for tourism and for learning about nations' history. Historical sites around the world are in damaged conditions due to various factors from the environment, man-made activities or natural calamities. To ensure safety and avoid further deterioration, digital reconstruction of heritage sites can be used to create 3D virtual models of these structures for archiving and for inspection purpose. This paper presents a technique to reconstruct a high-quality image-based 3D model of a heritage structure. An exemplar-based inpainting algorithm was used for removing deformable obstacles such as trees in 2D images since such obstacles are unwanted in a final 3D model. They also create noise in the 3D modeling process, which makes the final 3D model less accurate. In this paper, an inpainting algorithm is applied to generate implied texture to fill holes that occurred from removing objects so that the generated 3D model does not contain any hole and becomes watertight. The modified exemplar-based inpainting algorithm was implemented on 2D images to remove unwanted objects, and then the image-based 3D modeling technique was applied to create a 3D model that did not contain any unwanted objects. The results show that the final 3D model is more accurate when applied the object removal process and the model provides better visualization for heritage structures.