Você não pode combinar like e in. A declaração abaixo faria o trabalho:
Select * from Table1
where EmpPU NOT Like '%CSE%'
AND EmpPU NOT Like '%ECE%'
AND EmpPU NOT Like '%EEE%'
Select * from Table1
where EmpPU NOT Like '%CSE%'
AND EmpPU NOT Like '%ECE%'
AND EmpPU NOT Like '%EEE%'