seo – How to get duplicate geo-targetted sub-directories indexed when Google is ignoring the canonicals?

I have a main website example.com which is mainly used for targeting one country. We recently started creating sub-directories for targeting other countries i.e, example.com/us/, example.com/ph/ etc., We have replicated the same example.com and created sub-directories i.e, content and design are same. I have put canonical URL for sub-directories as example.com, as that is the primary domain.

Now, after optimizing sub directory pages based on country wise, I have changed certain sub directories canonical URL as example.com/us/ – My sub-directories are not getting crawled or indexed. In search console, it shows me the error – “Duplicate, submitted URL not selected as canonical”
I have changed canonical URLs but its been a month, the pages are not still not shown in the search results. What should I do to get my pages crawled?