In the SQL task, in order to use file names or field names that include special characters or periods , the names must be enclosed in double quotes when writing the SQL statements.
For example, given a library/schema called MYLIB which has a file named MY.FILE, the select statement would look similar to:
SELECT * FROM MYLIB.”MY.FILE”.
Of course all names may be enclosed in double quotes if so desired.
In the SQL Wizard, there is an option to generate the SQL Statements with Double Quotes (or database specific enclosing character) in the preview.