In an electromagnetic launcher (EML) system, a high amount of energy must be supplied in a short time period to provide the necessary acceleration for the projectile. This type of energy is generally provided by many capacitive pulsed power supply (CPPS) units that are connected in parallel. Since the shaping inductors of different modules are placed close by to achieve a compact design, their magnetic fields affect each other. If this magnetic coupling causes a high enough negative induced voltage in nonconducting modules, the freewheeling diode may fail if the particular module is fired as its diode is open. Thus, protection systems that avoid the activation of modules while their diodes are in conduction are used in EML systems. The protection system avoids the fault but decreases the supplied energy. This study proposes a design methodology that determines the positions and orientations of shaping inductors to avoid semiconductor faults with a compact power supply design. The design procedure starts by determining the physical dimensions of possible inductors considering the minimum inductance value and maximum allowed lateral electromagnetic force. Then, the distances between the inductors are systematically determined by an iterative approach by considering the different predefined orientations. In this method, 3-D FEA models are used to calculate the inductance matrix, which is then used to estimate the induced voltages in other inductors as well as in the system-level simulation models.