If you want to save data to a custom table/database, you can use any ORM tool you like.
But if you want to save IContent (pages, blocks, etc.), then you need to use IContentRepository: https://world.episerver.com/documentation/developer-guides/CMS/Content/icontentrepository-and-datafactory/
Can we do CRUD operations like MVC in EPIServer. Means in database i used multiple tables for inserting data with the use of clustured and non-clustered indexes. Is it possible in episerver, Could anybody suggest me?