mongodb aggregate nested nested array

You can try below aggregation with Mongo 3.4 version.

The below query finds the last item (-1) using $arrayElemAt operator in the ndr array and stores the variable in last using $let operator for each nodes and compare the last variable position value using $$ notation to 3 and wraps the nbr element within array [] if entry found and else returns empty array.

$map operator to reach nbr array inside the nodes array and project the updated nbr array while mapping the rest of nodes fields.

$addFields stage will overwrite the existing nodes with new nodes while keeping the all the other fields.

db.collection.aggregate([{
    $addFields: {
        nodes: {
            $map: {
                input: "$nodes",
                as: "value",
                in: {
                    node: "$$value.node",
                    name: "$$value.name",
                    ndr: {
                        $let: {
                            vars: {
                                last: {
                                    $arrayElemAt: ["$$value.ndr", -1]
                                }
                            },
                            in: {
                                $cond: [{
                                        $eq: ["$$last.position", 3]
                                    },
                                    ["$$last"],
                                    []
                                ]
                            }
                        }
                    }
                }
            }
        }
    }
}]);

Update:

You can try $redact which will keep the whole document if it finds the matching position from with the given filter.

$map to project the true, false values based on the filter for each of the nodes nbr position value and $anyElementTrue will inspect the previous boolean values for each doc and return a true or false value and $redact will use the booelan value from above comparison; true value to keep and false value to remove the document.

db.collection.aggregate([{
    $redact: {
        $cond: [{
            $anyElementTrue: {
                $map: {
                    input: "$nodes",
                    as: "value",
                    in: {
                        $let: {
                            vars: {
                                last: {
                                    $arrayElemAt: ["$$value.ndr", -1]
                                }
                            },
                            in: {
                                $cond: [{
                                        $eq: ["$$last.position", 3]
                                    },
                                    true,
                                    false
                                ]
                            }
                        }
                    }
                }
            }
        }, "$$KEEP", "$$PRUNE"]
    }
}]);