Yes you can.
Creating the map
Assuming you have created your MarkerClusterer object something like this:
var center = new google.maps.LatLng(10, 20);
var map = new google.maps.Map(document.getElementById('map'), { zoom: 6, center: center, mapTypeId: google.maps.MapTypeId.ROADMAP });
var markerClusterer = new MarkerClusterer(map);
Adding markers
You can add multiple markers to it something like this:
var markers = []
var marker = new google.maps.Marker({position: center});
markers.push(marker);
markerClusterer.addMarkers(markers);
Note that here I have added only one.
Removing all markers
You can then clear all the markers using clearMarkers something like this:
markerClusterer.clearMarkers();
markers = [];
Note that for tidiness I have also unset the markers array here.
Docs
Full documentation on all the available methods is available here:
https://googlemaps.github.io/js-marker-clusterer/docs/reference.html
UPDATED Link: https://googlemaps.github.io/js-markerclustererplus/classes/markerclusterer.html#clearmarkers
It’s a sensible and relatively complete API.