Demo of event handling and consuming events. Double click to add a rectangle. Selected rectangles have a gold border. Drag a rectangle to move it; drag on empty space to select.

RectangleDrawing.java

import java.util.ArrayList;
import java.util.List;
import java.util.stream.Collectors;

import javafx.application.Application;
import javafx.beans.property.ObjectProperty;
import javafx.beans.property.SimpleObjectProperty;
import javafx.collections.FXCollections;
import javafx.collections.ListChangeListener.Change;
import javafx.collections.ObservableList;
import javafx.geometry.Point2D;
import javafx.scene.Scene;
import javafx.scene.control.ColorPicker;
import javafx.scene.control.ScrollPane;
import javafx.scene.input.MouseEvent;
import javafx.scene.layout.BorderPane;
import javafx.scene.layout.Pane;
import javafx.scene.paint.Color;
import javafx.scene.shape.Rectangle;
import javafx.stage.Stage;

public class RectangleDrawing extends Application {

    private Pane pane;
    private ObservableList<Rectangle> selectedRects;
    private List<Rectangle> allRects;

    @Override
    public void start(Stage primaryStage) {
        pane = new Pane();
        pane.setMinSize(400, 400);
        selectedRects = FXCollections.observableArrayList();

        selectedRects.addListener((Change<? extends Rectangle> c) -> {
            allRects.forEach(r -> {
                if (selectedRects.contains(r)) {
                    r.setStroke(Color.GOLD);
                } else {
                    r.setStroke(Color.TRANSPARENT);
                }
            });
        });

        allRects = new ArrayList<>();

        ColorPicker picker = new ColorPicker();
        picker.setValue(Color.BLUE);
        picker.setOnAction(e -> selectedRects.forEach(r -> r.setFill(picker.getValue())));

        pane.setOnMouseClicked(e -> {
            if (e.getClickCount() == 2) {
                addNewRectangle(e.getX(), e.getY(), picker.getValue());
            }
        });

        Rectangle selectionRect = new Rectangle();
        selectionRect.setFill(Color.TRANSPARENT);
        selectionRect.setStroke(Color.BLACK);

        ObjectProperty<Point2D> mouseAnchor = new SimpleObjectProperty<>();

        pane.setOnMousePressed(e -> {
            mouseAnchor.set(new Point2D(e.getX(), e.getY()));
            selectionRect.setX(e.getX());
            selectionRect.setY(e.getY());
            selectionRect.setWidth(0);
            selectionRect.setHeight(0);
        });

        pane.setOnMouseDragged(e -> {
            selectionRect.setX(Math.min(e.getX(), mouseAnchor.get().getX()));
            selectionRect.setY(Math.min(e.getY(), mouseAnchor.get().getY()));
            selectionRect.setWidth(Math.abs(e.getX() - mouseAnchor.get().getX()));
            selectionRect.setHeight(Math.abs(e.getY() - mouseAnchor.get().getY()));
        });

        pane.setOnMouseReleased(e -> {
            selectedRects.setAll(
                allRects.stream()
                .filter(r -> r.getBoundsInParent().intersects(selectionRect.getBoundsInParent()))
                .collect(Collectors.toList()));
            selectionRect.setWidth(0);
            selectionRect.setHeight(0);
        });

        pane.getChildren().add(selectionRect);

        ScrollPane scroller = new ScrollPane(pane);

        BorderPane root = new BorderPane(scroller);
        root.setTop(picker);

        Scene scene = new Scene(root, 400, 400);
        primaryStage.setScene(scene);
        primaryStage.show();
    }

    private void addNewRectangle(double x, double y, Color color) {
        Rectangle rect = new Rectangle(x, y, 50, 50);
        rect.setFill(color);
        rect.setStroke(Color.TRANSPARENT);
        rect.setStrokeWidth(2);
        pane.getChildren().add(pane.getChildren().size() - 1, rect);
        allRects.add(rect);

        ObjectProperty<Point2D> mouseAnchor = new SimpleObjectProperty<>();

        rect.setOnMouseDragged(e -> {
            double deltaX = e.getX() - mouseAnchor.get().getX();
            double deltaY = e.getY() - mouseAnchor.get().getY();
            rect.setX(rect.getX() + deltaX);
            rect.setY(rect.getY() + deltaY);
            mouseAnchor.set(new Point2D(e.getX(), e.getY()));
            e.consume();
        });

        rect.setOnMousePressed(e -> {
            mouseAnchor.set(new Point2D(e.getX(), e.getY()));
            e.consume();
        });

        rect.setOnMouseReleased(MouseEvent::consume);

        selectedRects.setAll(rect);
    }

    public static void main(String[] args) {
        launch(args);
    }
}