Once you have filed a non-provisional application, you can expect to wait, under current Patent Office procedure, 2-3 years before a Patent Examiner reviews your application. After review, the Examiner will issue an Office Action which almost always is a challenge to the application.
Prior to sending an Office Action, a Patent Examiner will review your application and will conduct a patentability search to determine if your invention is new or different from what has been invented by others. The Examiner will compare the information uncovered in his or her search to the claims of your invention. While rare, it is possible that the Examiner will find an invention that was not uncovered during a preliminary patentability search which prevents you from having your patent granted.
In most cases, the Examiner will challenge the patentability of your invention by rejecting one or more of the claims. The Examiner will typically cite one or more prior patents and will argue that your invention, or a portion of your invention, is unpatentable in view of the prior patents. Based on standard Patent Office procedure, such a rejection is expected and can typically be overcome by argument and/or amendment to your claims.
A significant part of the patent application is the Claims section. The Claims are a formal description that describes the portions of your invention that are patentable. Most inventions are not wholly unique, but are an improvement upon a known invention. In such a case, the claims make clear that the inventor only claims rights in the given improvements over the prior invention.
The Office Action process either results in an allowed or rejected patent. If your patent is allowed, you are then required to pay an issue fee, after which the patent issues. If your patent is rejected you have several options that allow for you to continue fighting for your patent.