CMC vellore has TEM facility. You may need to approach officially.

in my department and in anna university only SEM facility is available and chennai cancer institute (3000 persample/ 15 days) TEM facility is available.

TNAU having both SEM and TEM facility facility is available.

animal science reserach institute (madras vertinary collage) TEM

facility is available.

IIT(M)also having SEM (SAIF lab)

National Centre for Nanoscience and Nanotechnology, University of Madras, Maraimalai (Guindy)Campus, Chennai-600025.

PSG COLLEGE IS BETTER CHOICE  

How much per sample in PSG?

Trichy National college has SEM facility. 

VIT has TEM Facility and also in CECRI TEM facility is available.

in CIT ramakrishna engineering college,coimbatore

refer the website for details

http://researchap.com/central-facilities-for-instrumentation-and-characterization-of-samples/

NIT, trichy

SEM testing available at Kalasalingam University, Krishnankoil

PSG and tamil nadu agricultural University coimbatore having TEM facilities with nominal cost

i think,agricultural university cost high compared to other institute

Anna university SEM,CIPET SEM,IIT chennai SEM,TEM,Bharatidasan FESEM,BHEL FESEm,Cross Beam ,SEM,SASTRA FEGTEM FESEM,Karunya,Kalasalingam,Annamalai university,CECRI karaikudi,MS university tirunelveli,PSG ,CIT,Amirtha,SITRA coimbatore,Bharatidasan

can i get sastra university contact number for SEM, TEM facilities

Though it is a late reply, thought it might be beneficial for someone else. CMC in Vellore has sample preparation,sectioning and imaging facility. And the images are very good. I had processed my samples there.

CMC has TEM which I had referred to in my previous answer.