The Scorch Trials are the actual trials that the Gladers are put through as they enter the desert, which is known as the Scorch. Now, the word "trial" can mean a few things: it can mean a court case, in which someone is either found guilty or innocent; but it can also mean a test or an examination.
This second definition of "trial"—a test or examination—is what we get in the title of this book. When you put it together—the Scorch being the desert area, and the trial being a test—then it's pretty easy to understand why this book is called The Scorch Trials.
In short, the title refers to the test the Gladers are put on in the Scorch.
But you already knew that.