dump this into a more specific collection of just the ids you don't want
var notTheseBarIds = filterBars.Select(fb => fb.BarId);
then try this:
fooSelect = (from f in fooBunch
where !notTheseBarIds.Contains(f.BarId)
select f).ToList();
or this:
fooSelect = fooBunch.Where(f => !notTheseBarIds.Contains(f.BarId)).ToList();