Malleable robots are a type of reconfigurable serial robot capable of adapting their topology, through the use of variable stiffness malleable links, to desired tasks and workspaces by varying the relative positioning between their revolute joints. However, their reconfiguration is nontrivial, lacking intuitive communication between the human and the robot, and a method of efficiently aligning the end effector to a desired position. In this article, we present the design of an interactive augmented reality (AR) alignment interface, which helps a malleable robot understand the user’s task requirements, visualizes to the user the requested robot’s configuration and its workspace, and guides the user in reconfiguring the robot to achieve that configuration. Through motion tracking of a physical two degree-of-freedom (2 DoF) malleable robot, which can achieve an infinite number of workspaces, we compute the accuracy of the system in terms of initial calibration and overall accuracy, and demonstrate its viability. The results demonstrated a good performance, with an average repositioning accuracy of 9.64 ± 2.06 mm and an average base alignment accuracy of 10.54 ± 4.32 mm in an environment the size of 2,000 mm × 2,000 mm × 1,200 mm.