You haven't specified enough about what your actual problem is, but I guess you're trying to cope with a feature that is missing in (some versions of) IE.
The main thing I would say is that your approach to solving the problem is fundamentally wrong.
For a start, the capabilities of IE (as for any other browser) vary wildly between the various versions. IE10 is actually pretty good, and supports most of the modern browser features you might want to use. And IE11 will be released in the near future with even better support. You might have a problem with IE8 or earlier, but most well-written code ought to work with IE10 without any problems. Therefore, a blanket check for IE without checking the version is almost certainly a bad idea.
Secondly, even if you are going to do an IE check, <![if !IE]>
is wrong because IE has dropped support for this since IE10. The reason they've dropped it is specifically to discourage the bad practice of browser detection.
There are various other ways of detecting IE, but they're all bad practice for the same reason: detecting the browser and making your site work differently for different browsers has a whole load of issues with it. It's a big topic, so I suggest reading here for more info.
Finally, what to do instead? The answer is feature detection.
In short:
- Work out what feature it is that you need that isn't supported in older browsers
- Write a script that detects whether the user's browser supports that feature.
- Write your code to cope with a negative answer from that check.
(this may include 'polyfill' scripts that add the missing features to the browser, or some kind of alternative functionality for unsupported browsers)
This technique allows you to write your site in a way that deals with all browsers regardless of what capabilities they have.
A good library you should try for feature detection is Modernizr.
ps - If you're having trouble with something specific in IE, you should ask a separate question about it; there's a good chance that the folk here will be able to help you get it working, and the whole 'how do I detect IE' question would be unnecessary anyway.