The Method of Manufactured Solutions (MMS) has proven to be useful for completing code verification studies. MMS allows the code developer to verify that the observed order-of-accuracy matches the theoretical order-of accuracy. Even though the solution to the partial differential equation is not intuitive, it provides an exact solution to a problem that most likely could not be solved analytically. The code developer can then use the exact solution as a debugging tool. While the order-of-accuracy test has been historically treated as the most rigorous of all code verification methods, it fails to indicate code “bugs” that are of the same order as the theoretical order-of-accuracy. The only way to test for these types of code bugs is to verify that the theoretical local truncation error for a particular grid matches the difference between the manufactured solution (MS) and the solution on that grid. The theoretical local truncation error can be computed by using the modified equation analysis (MEA) with the MS and its analytic derivatives, which we call modified equation analysis method of manufactured solutions (MEAMMS). In addition to describing the MEAMMS process, this study shows the results of completing a code verification study on a conservation of mass code. The code was able to compute the leading truncation error term as well as additional higher-order terms. When the code verification process was complete, not only did the observed order-of-accuracy match the theoretical order-of-accuracy for all numerical schemes implemented in the code, but it was also able to cancel the discretization error to within roundoff error for a 64-bit system.