Polygons merge with a hole.

From Mike's bl.ock on topojson.merge: now merge multiple polygons into a single polygon with a hole.

<!DOCTYPE html>
<meta charset="utf-8">
<style>

.state {
  fill: #ccc;
}

.state-boundary {
  fill: none;
  stroke: #fff;
}

.state.selected {
  fill: orange;
  stroke: #000;
}

</style>
<body>
<script src="https://d3js.org/d3.v3.min.js"></script>
<script src="https://d3js.org/topojson.v1.min.js"></script>
<script>

var width = 960,
    height = 600;

var projection = d3.geo.albersUsa()
    .scale(1280)
    .translate([width / 2, height / 2]);

var path = d3.geo.path()
    .projection(projection);

var svg = d3.select("body").append("svg")
    .attr("width", width)
    .attr("height", height);

var selected = d3.set([
   9, 10, 12, 13, 17, 18, 19, 21, 23, 24,
  25, 26, 29, 31, 33, 34, 36, 37, 39, 42,
  44, 45, 47, 50, 51, 55
]);

d3.json("/../../data/us.json", function(error, us) {
  svg.append("path")
      .datum(topojson.feature(us, us.objects.states))
      .attr("class", "state")
      .attr("d", path);

svg.append("path")
      .datum(topojson.mesh(us, us.objects.states, function(a, b) { return a !== b; }))
      .attr("class", "state-boundary")
      .attr("d", path);

svg.append("path")
      .datum(topojson.merge(us, us.objects.states.geometries.filter(function(d) { return selected.has(d.id); })))
      .attr("class", "state selected")
      .attr("d", path);
});

d3.select(self.frameElement).style("height", height + "px");

</script>

Modified http://d3js.org/d3.v3.min.js to a secure url

Modified http://d3js.org/topojson.v1.min.js to a secure url

Changed /mbostock/raw/4090846/us.json to a local referenece

https://d3js.org/d3.v3.min.js

https://d3js.org/topojson.v1.min.js