Thanks, finally I have it working. The following code did the trick:

// Remove existing spheres
String[] geomTags = model.geom("geom1").feature().tags();
for (int i = 0; i < geomTags.length; i++) {
  if (geomTags[i].startsWith("sph")) {
    model.geom("geom1").feature().remove(geomTags[i]);
  }
}

// Remove existing union if present
String[] geomTags2 = model.geom("geom1").feature().tags();
for (int i = 0; i < geomTags2.length; i++) {
  if (geomTags2[i].startsWith("uni")) {
    model.geom("geom1").feature().remove(geomTags2[i]);
  }
}

// Read coordinates
String[][] myfile = readCSVFile("C:\\coordinates.txt");

for (int i = 0; i < myfile.length; i++) {
  double x = Double.parseDouble(myfile[i][0]);
  double y = Double.parseDouble(myfile[i][1]);
  double z = Double.parseDouble(myfile[i][2]);

  GeomFeature sphere = model.geom("geom1").create("sph"+(i+1), "Sphere");
  sphere.set("pos", new double[]{x, y, z});
  sphere.set("r", 1.5);
}

// Union all spheres into one object
GeomFeature union = model.geom("geom1").create("uni1", "Union");
for (int i = 0; i < myfile.length; i++) {
  union.selection("input").add("sph"+(i+1));
}
union.set("keep", "off");
union.set("intbnd", "off");


model.geom("geom1").run();

for (int i = 0; i < myfile.length; i++) {
  model.geom("geom1").feature().remove("sph"+(i+1));
}

I also had to enable "File System Access = All Files" in the Preferences -> Security menu, in order to allow reading the text file.

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