Aggregation pipeline and indexes

From http://docs.mongodb.org/manual/core/indexes/#multikey-indexes, it is possible to create an index on an array field using a multikey index. http://docs.mongodb.org/manual/applications/aggregation/#pipeline-operators-and-indexes lists some ways of how an index can be used in aggregation framework. However, there may be times that I may need to perform an $unwind on an array field to perform a $group. My question is, are multikey indexes (or any index using such array field) can still be used once they are operated on in the middle of the pipeline?