Microsoft Surface tablet owners using a pen, stylus or finger as touch-mode for providing input to the device may find sometimes the screen doesn’t respond appropriately. Touch input is on by default and can’t be turned off. Probably there’s a change in accessibility settings and programs hence, you need to calibrate such settings. Also, check if you have correct drivers installed.
Calibrate Surface Pen and Touch Settings
To adjust how accurately your screen senses when you use a pen or finger, swipe in from the right edge of the screen, and then tap Search.
Enter Calibrate in the search box, tap Settings, and then Calibrate the screen for pen or touch input to open Tablet PC Settings. Check that the monitor shown in the Display field matches the screen you want to calibrate.
Tap Calibrate, and follow the on-screen instructions.
Get touchscreen to go to the correct screen
Follow the above mentioned steps (1,2 and 3). Next, tap Setup, and follow the on-screen instructions.
You can also change Pen and Touch actions, if you want to.
Change Pen and Touch actions
To change or adjust how fast, far, or long an action takes, swipe in from the right edge of the screen, and then tap Search.
Enter pen and touch in the search box, tap Settings, and then tap Pen and Touch. Tap the action you would like to configure, and choose Settings.
From there, simply follow the on-screen instructions to complete the task.
Sourced from Microsoft.
Check out the Surface Hub App too! It lets you customize the Surface Pro 3 Pen.
See this post if Windows laptop or Surface Touch Screen not working on Windows 8.1 device.