What solutions have you considered so far? Does your application figure out when the USB device is plugged in or unplugged?
As far as I know, there's no native support in .Net for directly accessing USB devices. I had to use libraries such as LibUsbDotNet (http://sourceforge.net/projects/libusbdotnet/) or SharpUSBLib (http://www.icsharpcode.net/OpenSource/SharpUSBLib/) There were pros and cons to both in terms of samples, documentation etc. I am sure you will be able to find what suits you best.
In one case I was able to connect to the device using WMDC, once the connection was established I used OpenNETCF RAPI library to read from / write to the device.
Here's another excellent resource that I had found useful when I wrote an application that needed to interact with a USB device (a barcode scanner).
http://www.developerfusion.com/article/84338/making-usb-c-friendly/
There was a good resourceful discussion to a similar question here on Stackoverflow : Working with USB devices in .NET