Abstract Cardiac trabeculae are fine rod-like muscles whose ends are attached to the inner walls of ventricles. Accurate extraction of trabeculae is important yet challenging, due to the background noise and limited resolution of cardiac images. Existing works proposed to handle this task by modeling the trabeculae as topological handles for better extraction. Computing optimal representation of these handles is essential yet very expensive. In this work, we formulate the problem as a heuristic search problem, and propose novel heuristic functions based on advanced topological techniques. We show in experiments that the proposed heuristic functions improve the computation in both time and memory