In the BITS HD exam, notification syllabus for instrumentation is given separately, do BITS conduct a separate paper for instrumentation engineers and if so, will I be eligible to get microelectronics

Yes. The students from Instrumentation are also eligible to get Microelectronics at Pilani Campus. There is not any separate paper for Instrumentation engineers. The students can also get BITS Pilani through GATE Score.

Eligibility:

The eligibility to get ME in Microelectronics as available on the official website of the institution is Integrated First Degree of BITS in

1. Electrical & Electronics
2. Electronics & Instrumentation
3. Electronics & Communication
4. Computer Science
5. Physics or equivalent

The Students applying with Integrated First Degree of BITS Pilani or its equivalent will be considered for admissions to any M.E. Programme with the requirement of opting for additional programs. 

Examination Pattern:

Given below is a brief insight into the examination pattern.

BITS does not conduct a separate examination for Instrumentation Engineering. You can take admission in Microelectronics at BITS Pilani campus through BITS HD. 

Even if you are from Instrumentation Engineering you will have Microelectronics as a choice for specialization. I have a few friends who are from Instrumentation background and pursuing Microelectronics at BITS Pilani.