This paper presents a direct 3D visual servo scheme for the automatic alignment of point clouds (respectively, objects) using visual information in the spectral domain. Specifically, we propose an alignment method for 3D models/point clouds that works by estimating the global transformation between a reference point cloud and a target point cloud using harmonic domain data analysis. A 3D discrete Fourier transform (DFT) in $\mathbb{R}^3$ is used for translation estimation and real spherical harmonics in $SO(3)$ are used for rotation estimation. This approach allows us to derive a decoupled visual servo controller with 6 degrees of freedom. We then show how this approach can be used as a controller for a robotic arm to perform a positioning task. Unlike existing 3D visual servo methods, our method works well with partial point clouds and in cases of large initial transformations between the initial and desired position. Additionally, using spectral data (instead of spatial data) for the transformation estimation makes our method robust to sensor-induced noise and partial occlusions. Our method has been successfully validated experimentally on point clouds obtained with a depth camera mounted on a robotic arm.