[{"_id":ObjectId("562e7c594c12942f08fe4192"),"shapes":[{"shape":"square","color":"blue"},{"shape":"circle","color":"red"}]},{"_id":ObjectId("562e7c594c12942f08fe4193"),"shapes":[{"shape":"square","color":"black"},{"shape":"circle","color":"green"}]}]

db.collection.aggregate([{$set:{shapes:{$filter:{input:"$shapes",as:"shape",cond:{$eq:["$$shape.color","red"]}}}}},{$match:{$nor:[{shapes:{$exists:false}},{shapes:{$size:0}}]}}])