Print out your manuscript and hide it somewhere for at least two weeks (preferably a month or more). It sounds counterintuitive, because finally finishing your manuscript will probably give you a surge of energy, but it's important to put some distance between you and your work. After a few weeks away, you'll be able to look at your manuscript with fresh eyes.
Read your manuscript once or twice without donning an editor's hat. Don't have a pen in your hand. Just try to experience and enjoy the book as a reader would, and make simple notes of any plot holes you notice or things that don't add up. Experience the big picture of your story before getting into the nitty-gritty.
Start your edit with the simple stuff. You probably noticed when you read your manuscript that spelling errors and grammatical missteps jumped right out at you. Your first edit should be a sweeping copyedit to clean up all the little typos you missed when you were writing. Start thinking about the rhythm of your sentences. Did you notice that you use the same sentence constructions or paragraph patterns (e.g., two long paragraphs followed by a very short one) over and over?
Hatch a plan for fixing the big issues. Are there any full scenes you need to add? Perhaps a good chunk of backstory is needed for one of your characters, or the ending happens way too fast to be satisfying. Plot where these scenes should go before writing them. Does this new information change any of the later scenes? Outline the major rewrites to keep track of them and ensure continuity.
Seek out feedback. Once you've completed a broad self-edit, it's time to give your manuscript to a trusted friend or your workshop group. Don't do this before you self-edit, because you want to have a good idea of the strengths and weakness you perceive before handing your work to someone else. That way, you'll know if your readers are having a completely different experience than you had hoped or intended.