How do i...select last 3 raw in this query

Have you experimented with TOP? What were the results?

SELECT TOP 3 Row_Number()...

Updated. The last 3 rows can be achieved if you reverse the ORDERing you have in place. Here is the full query based upon this:

;WITH emp_hierarachy AS(
	SELECT	emp = EmployeeId, EmployeeId, Manager, Firstname + ' ' + surname as [name], Position
	FROM		tblEmployee
		UNION ALL
	SELECT	rs.emp, t.EmployeeId, t.Manager, t.Firstname + ' ' + surname as [name], t.Position
	FROM		tblEmployee     t
	INNER JOIN emp_hierarachy rs ON t.EmployeeId = rs.Manager
)

	SELECT	TOP 3 id = Row_Number() OVER (ORDER BY (SELECT 1))
		,	rs.name
		,	rs.Position
	FROM		emp_hierarachy     rs
	WHERE	rs.emp = 179 
--	AND	rs.EmployeeId	!= rs.emp 
	ORDER BY ID -- DESC

Notes/Questions/Questions
Please note that the name field is wrapped in square brackets. Name is one of them words that is certain contexts is special.I generally would avoid using them.

In your commented out AND clause, you are using != for inequality. While this is valid in SQL Server, the ANSI standard is to use <>; so the portability of this code may be limited.

The CTE seems to be gathering more data than it needs to; only the EmployeeID, [name] and position columns are called upon, and the UNION ALL is going to add in duplicate records.

I would be interested in seeing sample data and the results you expect to come out; as I do not know the schema of these tables but I think this could be greatly reduced codewise

SELECT TOP 3 Row_Number() ... ORDER BY id ASC