I hope it goes without saying that the best thing you can do for your manuscript is to have it looked over by a professional editor. The cost of line- or copy-editing is an investment that will make your story, or novella, or novel the best it can be, and give it the greatest chance of success, whether you are self-published or intend to go down the traditional print publishing route.
That said, there are some things you can do on your own that will weed out some of the more egregious errors – the kind of things that will have slushpile readers dreaming of stapling your title page to your forehead.
Obvious, right? But you’d be surprised how many aspiring authors fail to do even this simple a task. No spell-checking tool is infallible. Even the most robust dictionary has its limitations, although most of them can be added to if they don’t recognise a certain word in your manuscript. Just be sure that you have definitely spelled it correctly yourself.
The other weakness with a spell-checker is its inability to recognise homographs, homophones, and homonoyms. These are words that are either spelled the same, but have a different meaning, are pronounced the same, but have a different meaning, or both. The problem, of course, is that your spell-checker is only making sure the word is spelled correctly – it is not trying to attach any meaning to it. It will run right past weather and whether in a sentence, and will gloss over peek, pique and peak without a second glance.