Hello Neha

Yes, in order to get admission for para- medical courses( physiotherapy as you specified), you have to use your NEET UG scorecard. For physiotherapy, the lowest marks required are somewhat around 160-170 and the cutoff can go as high as 640-650  ( it depends on the college though). You can also go for private institutions and appear for their entrance tests for para-medical courses. 
 I hope this helps.