I am trying to copy a file in one folder in source bucket to another folder in the same bucket under source folder using boto3. 
Source bucket: Testing
Source Path: A/B/C/D/E/F..
I have some files in C, which I need to move to E. 
My problem is, lambda is running in loop for this. I have this lambda which get triggered when my file comes to C, and then ut trigger another one to do something else. Now between these two, I have to move the file from C to E and then trigger the lambda to perform next operation. 
Anyone have any insight how I can fix that issue of lambda running in loop?
In S3 there is no folder. You'd better see it as a bucket-key-value. The folder-like representation you see in the console is just a visualisation.
Your Lambda is triggered by an event of file modification in your bucket. You have to play with the prefix and the suffix of the S3 event.
Do you control the name of the file you put in S3?

Yes. Suppose your filename always starts with new. Set your event with prefix: A/B/C/new. When a file get in A/B/C/new... the lambda is triggered because it matches the prefix, when the same files goes to A/B/C/D/E/new... no lambda is triggered because the prefix doesn't match.
No. Then change your folder hierarchy. Set your event with prefix: A/B/C/. Move the file to any key (i.e. "folder") that doesn't start with A/B/C, for example A/B/E. Thus, the second key will not match the prefix.

The suffix is not of any help unless you may rename the suffix of the file. If you are able to rename the file you create an event with suffix: .abc, and when moving the file you rename it to something ending in .xyz. Thus only the .abc files will trigger the Lambda, wherever they are situated.
Copy files in nested folders in S3 bucket