You can't do it using MTM (no matter which version you are using).
Using TFS 2012 the only way is to use TFS-API, here a short example how to check if a particular Test Case is a part of any Test Suite:
using Microsoft.TeamFoundation.Client;
using Microsoft.TeamFoundation.TestManagement.Client;
// Current user credentials will be used to access to TFS
TfsTeamProjectCollection tfsCollection = TfsTeamProjectCollectionFactory.GetTeamProjectCollection(new Uri(<TFS Url>));
tfsCollection.EnsureAuthenticated();
ITestManagementService testManagementService = tfsCollection.GetService<ITestManagementService>();
ITestManagementTeamProject teamProject = testManagementService.GetTeamProject(<team project name>);
// Get all Test Suites your Test Case belongs to
// (Across all Test Plans in the Team Project)
ITestSuiteCollection testSuites = teamProject.TestSuites.ReferencingTestCase(<test case id>);
bool doesItBelongToAnyTestSuite = testSuites.Any();
If you would use TFS 2013 it will be possible to achieve this using Work Item queries since Test Plan and Test Suite become Work Items with TFS 2013 Update 3 (RC was released on 2. July 2014).