Hi Kalyanee, I use CTEs extensively, I think it just depends on the specific query.
If you are encountering subquery row limit issues, then you can potentially use MSQ to run the queries with the sortMerge join method, which does not use broadcast joins and will avoid that problem.
Otherwise if you are just having a general performance or logic issue getting the query to do what you want, feel free to post it so we can take a look.
Thanks. John