Leaflet map distance from the onclick marker
A short review;


selPts.length = 0; //Reset the array if selecting new points always resets the array, even if no points will be added, also selPts = [] is more idiomatic
Seems like xy is not declared there, and it probably should be. Nor is selPts
I feel center describes more accurately the purpose of xy
Idiomatic JavaScript uses lowerCamelCase, so layer_lat_long -> layerLatLong etc. 
In the end I went with layerLatLng since you get it from a function called getLatLng
I only knew selPts was selectedPoints due to comments, I think you should spell it out completely
You can extract the common logic into a function and pass that function to .eachLayer()


Obligatory rewrite:

function SelectPoints(latitude, longitude) {
  var dist = document.getElementById("miles").value,
    theRadius = parseInt(dist, 10) * 1609.34; //1609.34 meters in a mile

  center = [latitude, longitude]; //center point of circle
  selectedPoints.length = []; //Reset the array if selecting new points

  function updateSelectedPoints(layer){
    // Lat, long of current point as it loops through.
    layerLatLng = layer.getLatLng();
    // Distance from our circle marker To current point in meters
    distanceFromCenter = layerLatLng.distanceTo(center);
    // See if meters is within radius, add the to array
    if (distanceFromCenter &lt;= theRadius){
      selectedPoints.push(layer.feature);
    }
  }

  if($('#cf').is(":checked")){
    job.eachLayer(updateSelectedPoints);
  }
  if($('#vm').is(":checked")){
    job2.eachLayer(updateSelectedPoints);
  }
  if($('#bt').is(":checked")){
    job3.eachLayer(updateSelectedPoints);
  }
}