Processing files with streams
From a good look;


Your indentation is horrendous, it makes your question hard to review. Please do consistent indentation. Use http://jsbeautifier.org/ if you cannot be bothered. 
It would have been good to document what the transformer does (drop 2 last characters)
I would have one-lined this:

 _transform(chunk,enc, transformed) {
   // process files here 
      let data=chunk.toString();
       data=data.substring(0,data.length-2);
        this.push(data);
         transformed();
}


to 

// process files here 
transform(chunk, enc, transformed) {
  this.push(chunk.toString().slice(0,-2));
  transformed();
}

If you are going to call in a handler 1 function with a signature that matches the handler like here:

stream.on('error', function(err) {
  reject(err);  });
});


then consider to use that function as the callback:

stream.on('error', reject);

When I take a step back, then I don't like the approach. You have this modern approach of the stream which is flowing data. Then you take the stream, plug it until your entire transformation is done, and then let it flow again. I might actually try to rewrite this. 


I rewrote all that code, this is how streams should work: pipe your file into your transform and pipe that to stdout.

"use strict";

let fs=require('fs'),
    filePaths=['./smurf.js','./gargamel.js'];

const Stream = require('stream');
const Transform = require('stream').Transform;

const myTransform = new Transform({
  transform(chunk, encoding, callback) {
    callback( null, chunk.toString().slice(0,-2) ); 
  }
});

filePaths.forEach(function (path) {
  fs.createReadStream(path).pipe( myTransform ).pipe( process.stdout );
});