Let me understand your question. Your website is indexed but when you check on the search engine your website won't appear on the search result, right?
So here is my advice first you need to check your search console.
Search Console > Search Analytics > Download the report, then you will have a clear idea of your keywords ranked, anchor text, position, CTR and so on.
Organize your keywords by themes and then start to optimize your site with those themes/keywords.