How do I calibrate a touchscreen on a dual monitor system?

As Beni Cherniavsky-Paskin suggested in a comment, I used the following command to map an input device to an output screen:

xinput map-to-output <device> <output>

To figure out which is which, I first ran xinput to list the input devices. From that listing, I observed that my touchscreen was "QUANTA Optical Touch Screen" and listed as device id 12. I then ran xrandr to determine the touchscreen, which in my case was VGA1.

Simply entering the following command then did the trick:

xinput map-to-output 12 VGA1

As Beni Cherniavsky-Paskin and Paul Lammertsma suggested in above comments xinput map-to-output <device> <output> did the trick for me!

you first need to run xinput to get the id of inupt device,

the above command return something like this for me.

user@user-hpEnvy:~$ xinput
⎡ Virtual core pointer                      id=2    [master pointer  (3)]
⎜   ↳ Virtual core XTEST pointer                id=4    [slave  pointer  (2)]
⎜   ↳ Logitech Unifying Device. Wireless PID:401b   id=10   [slave  pointer  (2)]
⎜   ↳ Logitech Unifying Device. Wireless PID:4016   id=11   [slave  pointer  (2)]
⎜   ↳ ELAN20E7:00 04F3:20E7                     id=13   [slave  pointer  (2)]
⎜   ↳ SynPS/2 Synaptics TouchPad                id=15   [slave  pointer  (2)]
⎣ Virtual core keyboard                     id=3    [master keyboard (2)]
    ↳ Virtual core XTEST keyboard               id=5    [slave  keyboard (3)]
    ↳ Power Button                              id=6    [slave  keyboard (3)]
    ↳ Video Bus                                 id=7    [slave  keyboard (3)]
    ↳ Video Bus                                 id=8    [slave  keyboard (3)]
    ↳ Power Button                              id=9    [slave  keyboard (3)]
    ↳ HP Truevision HD                          id=12   [slave  keyboard (3)]
    ↳ AT Translated Set 2 keyboard              id=14   [slave  keyboard (3)]
    ↳ HP Wireless hotkeys                       id=16   [slave  keyboard (3)]
    ↳ HP WMI hotkeys    

Next I ran xrandr to get the list of screens and the output of the command is like this

user@user-hpEnvy:~$ xrandr
Screen 0: minimum 8 x 8, current 3840 x 1080, maximum 32767 x 32767
eDP1 connected 1920x1080+0+0 (normal left inverted right x axis y axis) 382mm x 215mm
   1920x1080      60.0*+   59.9     40.0  
   1680x1050      60.0     59.9  
   1600x1024      60.2  
   1400x1050      60.0  
   1280x1024      60.0  
   1440x900       59.9  
   1280x960       60.0  
   1360x768       59.8     60.0  
   1152x864       60.0  
   1024x768       60.0  
   800x600        60.3     56.2  
   640x480        59.9  
HDMI1 connected primary 1920x1080+1920+0 (normal left inverted right x axis y axis) 600mm x 340mm
   1920x1080      60.0*+   50.0     59.9  
   1680x1050      59.9  
   1600x900       60.0  
   1280x1024      60.0  
   1440x900       59.9  
   1280x720       60.0     50.0     59.9  
   1024x768       60.0  
   800x600        60.3  
   720x576        50.0  
   720x480        60.0     59.9  
   640x480        60.0     59.9  
   720x400        70.1  
VIRTUAL1 disconnected (normal left inverted right x axis y axis)

In my case the touch device is ELAN20E7:00 04F3:20E7 id=13 and touch enabled screen is eDP1 to fix the issue i need to map the device the that monitor only for that i ran this command xinput map-to-output 13 eDP1

Problem solved and its working fine again :)

I am using elementary OS freya, so it should work for all distros based on Ubuntu 14.04 LTS

Very hard to find solution but actually pretty straight forward, just follow the answer from 'phnomic' here: Touchscreen and additional external monitor. Works flawless with my Fujitsu T730 with all kinds of external monitors!