Three-dimensional (3D) visualization of spatial and non-spatial data is a well-established practice having numerous applications. The cheapest and the most efficient way to 3D visualization is 3D images/ Anaglyphs. 3D images contain 3D information of the objects present in the image. These images are easily obtained by superimposing left and right eye images in different color in a single image. In this paper, a novel security framework, viz., watermarking scheme, is presented to ensure their security. The proposed security framework is employed in fractional Fourier transform domain of secret color channel followed by the embedding using singular value decomposition. The secret channels (SEC) are obtained by applying reversible integer transform on the RGB channels. The experimental results prove the robustness and imperceptibility of the proposed watermarking scheme. © The Visualization Society of Japan 2010.