You need to switch the control to pop-up window before doing any operations in it. By using this you can solve your problem.
Before opening the popup window get the handle of main window and save it.
String mwh=driver.getWindowHandle();
Now try to open the popup window by performing some action:
driver.findElement(By.xpath("")).click();
Set s=driver.getWindowHandles(); //this method will gives you the handles of all opened windows
Iterator ite=s.iterator();
while(ite.hasNext())
{
String popupHandle=ite.next().toString();
if(!popupHandle.contains(mwh))
{
driver.switchTo().window(popupHandle);
/**/here you can perform operation in pop-up window**
//After finished your operation in pop-up just select the main window again
driver.switchTo().window(mwh);
}
}