delete temporary files in postgresql

The temporary files that get created in base/pgsql_tmp during query execution will get deleted when the query is done. You should not delete them by hand.
These files have nothing to do with temporary tables, they are use to store data for large hash or sort operations that would not fit in work_mem.

Make sure that the query is finished or canceled, try running CHECKPOINT twice in a row and see if the files are still there. If yes, that's a bug; did the PostgreSQL server crash when it ran out of disk space?

If you really have old files in base/pgsql_tmp that do not get deleted automatically, I think it is safe to delete them manually. But I'd file a bug with PostgreSQL in that case.

There is no way to avoid large temporary files if your execution plan needs to sort large result sets or needs to create large hashes. Cursors won't help you there. I guess that with for-loops you mean moving processing from the database to application code – doing that is usually a mistake and will only move the problem from the database to another place where processing is less efficient.

Change your query so that it doesn't have to sort or hash large result sets (check with EXPLAIN). I know that does not sound very helpful, but there's no better way. You'll probably have to do that anyway, or is a runtime of several hours acceptable for you?