There are some applications that are only for i386 version but I have amd64 version.
Can I run them on my system?
I am using Kubuntu 12.04.1 LTS 64-bit version.
I think you can install the 32bit libraries, this may be enough.
Or for a custom job with lots of dependencies, there is debootstrap (puts a 32 or 64 bit image of minimal Debian, including apt-get (so you can add more), on to your hard disk, in its own subdirectory). multistrap does the same for other apt based distros e.g. ubuntu. Then you need something like schroot, to help launch the apps.