I would create a nice MVVM design. The ViewModel would have an ObservableCollection FileList, where File would hold whatever information you want. This class would have also an IsFileSelectedUI property so that you could right in your code. Then in XAML things are easy:
<ScrollViewer Grid.Column="0" Grid.Row="1" >
<ItemsControl ItemsSource="{Binding FileList}">
<ItemsControl.ItemTemplate>
<DataTemplate>
<Border BorderBrush="Gray" BorderThickness="1" Margin="2" Padding="2">
<StackPanel Orientation="Horizontal">
<CheckBox IsChecked="{Binding IsFileSelectedUI , Mode=TwoWay}"/>
<TextBlock Text="{Binding FileName}"/>
</StackPanel>
</Border>
</DataTemplate>
</ItemsControl.ItemTemplate>
</ItemsControl>
Then things are just as easy as:
FileList.Where(file=>file.IsFileSelectedUI)
etc
If I understood what you said :)