You've asked two questions:
1> How do I make it so only my program uses Fiddler?
2> How do I hide traffic from other programs?
For #1, you configure Fiddler so that it's not the system proxy (e.g. untick File > Capture Traffic) and then you manually configure your application to use the proxy using any mechanism available. That mechanism will depend on what the application uses for networking; e.g. you can set the .Proxy property on HTTPWebRequest objects if using .NET, or set the command line arguments for Java applets, etc.
For #2, there are many ways to do this. The simplest would be to click Rules > Customize Rules and scroll to OnPeekAtRequestHeaders
. Uncomment the block and add two lines inside it:
var sProc = ("" + oSession["x-ProcessInfo"]).ToLower();
if (!sProc.StartsWith("mylowercaseappname")) oSession["ui-hide"] = "NotMyApp";
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