How to convert my mkv files so it goes on iTunes?

These mkv files are 24 minutes to 2 hours long. I need a program that won't make watermarks, won't have a length limit, or anything unwanted added to the video.

Just conversion to mkv to mp4, nothing else (I can't seem to find any!).

If you can, Id like it to be free and not a trial thats limited or has missing features. A simple and easy to use program that you trust, like and use

I just really want these files converted… I've been looking all day and my day ended in disappointment. Could you please help me out…

Things I have tried:
http://www.convertmkv.net/mkv-to-mp4
VLC Media Player (Converter)
http://www.online-convert.com/

I wanted these files to be on my iPhone 4S. I have Windows 8 (If that helps). I got the mkv files downloaded from kickass.to.

Added (1). I tried handbrake but all it says scan failed and now I can't convert it.

Try HandBrake
http://handbrake.fr/

It will convert anything to anything for free.

I recommend using http://www.freemake.com/free_video_converter/
It's completely free and has no watermarks.
I use it all the time to convert mkv to mp4
It's also the easiest thing to use.

There are some best video converters available for you. They are listed below.
1. MPEG Streamclip
MPEG Streamclip is a powerful video player, editor, and conversion tool for Mac and Windows. It's great at transcoding, but it's also a great organizational tool for all of your video and media. If you opt to use it as a player, you can play all manner of video files through it, but from a video transcoding and conversion perspective, it's fast, flexible, and completely free.

2. Format Factory
Format Factory is a free, richly featured video conversion tool that can convert a laundry list of video formats to a wealth of popular, supported formats. Its interface leaves a bit to be desired, but it offers you a ton of conversion options and tweaks to make sure all of your videos are the same, or each video is just right. The utility even promises to repair broken audio or video if it can process it. You can use quick presets to convert videos for mobile devices, and even rip DVDs.

3. Handbrake
Video conversion and transcoding is actually Handbrake's bread and butter. Even though it's useful for a ton of other things (not to mention it's your favorite DVD ripping tool), at its core it does a fantastic job of converting and transcoding video from one format to another, while giving you all the features, tweaks, and options you need to make sure it plays smoothly on whatever device or screen you plan to send it to. It's one of those tools that has single push-button options if that's what you want, or deeper tweaks if you prefer those.

4. Freemake Video Converter
Freemake Video Converter is, as the name implies, completely free, and a great tool if you're looking for more options than you could possibly need in a package that's actually really attractive and fun to use. Freemake supports over 200 video formats and outputs in virtually every popular format you can think of, and can even convert online videos to mp3. There are simple presets for iOS and Android devices, as well as other tablets, handheld game consoles, and other devices.
Or You may take a look at this website, it collects 18 online video converters. Free without any limitation and watermark, no need to download anything, I'm sure you will find one you need. I personally prefer to using zamzar.com

Assuming that you are talking about MKV files with video encoded using the H.264/AVC or X.264 codec, and audio encoded using AAC or MP3 codec (which iTunes can play):

In Windows, use the freeware tool MKVtoMP4 to repack the video and audio streams into an MP4 container. Repacking / rewrapping means that the video/audio data is not being transcoded (re-encoded / re-compressed), so there's no quality loss in this stage. Download and instructions:
http://forum.videohelp.com/threads/340675-Mkv%C3%90%C2%A2%C3%90%C2%BEMp4-v0-224-rapid-tool-for-repack-Mkv-to-Mp4

Video Converter Platinum http://www.video-dvd-ripper.com/video-converter/ can convert MKV to iPhone 4s videos easily.