Normally, when you print a PDF that contains layers, just the content that is visible onscreen is printed. However, the creator of a layered PDF can control what prints, regardless of its visibility onscreen. The PDF creator can require that watermarks print or prevent the printing of confidential information. If the document is designed to print differently from how it currently appears onscreen, a message may appear in the Print dialog box. The Preview image in the Print dialog box always shows the page as it will print.
To work with layers in Acrobat, convert the source document to PDF using a preset that preserves layers, such as Acrobat 6 (PDF 1.5) or later.
1. Select the Layers icon 
in the Navigation panel. If the Layers icon isn't visible, do the following:
(Windows) Select the hamburger menu and then select View > Show/Hide > Navigation Panes > Layers.
(macOS) Select View > Show/Hide > Navigation Panes > Layers.
2. Choose Apply Print Overrides from the Options menu.
Depending on the visibility settings specified when the PDF was created, Apply Print Overrides may be unavailable in the Options menu.
1. Select the Layers icon in the Navigation panel. If the Layers icon isn't visible, do the following:
(Windows) Select the hamburger menu and then select View > Show/Hide > Navigation Panes > Layers.
(macOS) Select View > Show/Hide > Navigation Panes > Layers.
2. Expand the Layers area, select a layer, and then select Layer Properties from the Options menu 
3. In the Layer Properties dialog box, choose one of the following from the Print pop-up menu:
Always Prints Forces the layer to print.
Never Prints Forces the layer not to print.
Prints When Visible Matches printed output to onscreen visibility.
In Reader, you can open the Layer Properties dialog box, but you cannot change the settings.
A PDF can contain a set of print presets, a group of document-specific values that is used to set basic print options. By creating a print preset for a document, you can avoid manually setting certain options in the Print dialog box each time you print the document. It’s best to define print settings for a PDF at the time that you create it. However, print presets provide a means to add basic print settings to a PDF at any time.
1. (Windows) From the upper left, select the hamburger menu > select Document Properties, and then select the Advanced tab.
(macOS) Select File > Document Properties > Advanced.
2. In the Print Dialog Presets section, set options and click OK.
The next time you open the Print dialog box, the values will be set to the print preset values. These settings are also used when you print individual PDFs in a PDF Portfolio.
To retain a print preset for a PDF, save the PDF after creating the print preset.
Page Scaling Prepopulates the Page Scaling menu in the Print dialog box with the option you choose:
Default Uses the application default setting, which is Shrink To Printable Area.
None Prevents automatic scaling to fit the printable area. Use this setting to preserve the scale in engineering documents or the point size required for legal reasons.
The Page Scaling menu in the Print dialog box shows additional options, but you cannot prepopulate the dialog box with any of those options. Choose one of those options when you print.
DuplexMode For best results, the selected printer should support duplex printing if you select a duplex option.
Simplex Prints on one side of the paper.
Duplex Flip Long Edge Prints on both sides of the paper; the paper flips along the long edge.
Duplex Flip Short Edge Prints on both sides of the paper; the paper flips along the short edge.
Paper Source By Page Size Selects the option by the same name in the Print dialog box. Uses the PDF page size to determine the output tray rather than the page setup option. This option is useful for printing PDFs that contain multiple page sizes on printers that have different-sized output trays.
Print Page Range Prepopulates the Pages box in the Print Range section of the Print dialog box with the page ranges you enter here. This setting is useful in a workflow where documents include both instruction pages and legal pages. For example, if pages 1–2 represent instructions for filling out a form, you can set up your print job to print only the form.
Number Of Copies Prepopulates the Copies box in the Print dialog box. Choose a number from 2 to 5, or choose Default to use the application default, which is one copy. This limitation prevents multiple unwanted copies from being printed.
Start with these troubleshooting tips
Printing problems can have various causes. To identify the issue, start with this helpful TechNote: Troubleshoot PDF printing | Acrobat, Reader.
The PDF is password protected, and printing is not allowed
If you receive a password-protected PDF, enter the designated password to print the document. Some protected documents have restrictions that prevent you from printing, editing, or copying content in the document. If a document has restrictions on printing, contact the PDF author.
(Windows only) Protected Mode is interfering
The default Protected Mode greatly enhances the security of Reader. To determine if Protected Mode is interfering with printing, temporarily disable it: Right-click the document, and choose Page Display Preferences. Then click General on the left, and deselect Enable Protected Mode At Startup. Close Reader, restart it, and try to print the document again.
To ensure maximum security, when you finish printing, reselect Enable Protected Mode At Startup.
If Adobe Reader is prompting you to save a file when you click Print, then click Advanced in the Print dialog and deselect the Print to File option.
Note:
There are certain annotations (example: pop-up notes) which are available on the PDF document and the annotations do not print by default unless you want them to be printed.
This has been intentionally designed so that such annotations do not hinder the view of the content available behind them.
However, there may be cases when you do want them to be printed. To print the pop-up notes and other annotations:
This could happen due to an Adobe Acrobat installation file corruption. In order to resolve this issue, ensure you are using the latest version of Adobe Reader/ Acrobat application.
If you are seeing this issue with the latest version: