Protocase Resources

The information below is intended to be helpful for customers who wish to learn more about enclosure design. Also, please use our online support if you have questions for our expert design staff.


How to Design Custom Enclosures for Motherboard-Based Systems

If you're looking to integrate a standard form factor motherboard into your custom enclosure, the common ATX motherboard is universal, powerful, and cost-effective. Also, micro-ATX and mini-ITX motherboards have been developed specifically for applications where small size, low power consumption and minimal noise is desired. This resource will cover the key elements of designing custom enclosures that accommodating ATX, Micro-ATX and Mini-ITX motherboards. It also provides essential details such as dimensions, mounting the boards, and how to access input/output (I/O) connectors.

Note: Many of the concepts in this resource also apply when designing enclosures for other motherboard form factors and custom built circuit boards as well.

For simplicity, in this resource, we will assume the board is being mounted horizontally, on the base of the enclosure and the I/O connectors are accessed through the rear of the enclosure. However, if you choose alternate orientations, the same principles and details can be adapted.


If you are familiar with this resource and would like to design a custom enclosure using our free CAD software, Protocase Designer click here.


  • Figure 1 - ATX Board with PCI Cards

  • Figure 2 - ATX Board with PCI Cards

  • Figure 3 - ATX Board with PCI Cards

Note: If you intend to use a fan-cooled processor in a situation with little clearance between the fan and the enclosure wall, we recommend fans that pull air directionally across the processor heat sink rather than down onto the top of the sink.


Consider the orientation of fans carefully. Align intake and exhaust outlets so you can take advantage of the current they create, and make sure they don't conflict with heat sink fan flow. You can gain better air flow across the top of the board - on its way through the enclosure if you arrange the intake and exhaust cutouts accordingly.

See Figure 5 below for some examples of ventilation cutout placements.

To maximize the effect of ventilation airflow, ensure the only openings in your enclosure are the ventilation cutouts or openings that will be filled by switches, connectors, or panel display features.

Unnecessary holes in the enclosure panels can cause disruption of natural convection currents, resulting in less effective cooling of the processors. When in doubt - use a fan or fans to move air in and out of your enclosure.

The required volume of cooling air can be calculated as Volume (CFM) = 3.16 x Max Heat (watts) / ΔT (F), where Max Heat is the maximum sustained power dissipation of boards and components inside the enclosure, and ΔT is the maximum allowable temperature rise.

Designs with air intake cutouts in the bottom panel should include feet to raise the enclosure off of its support surface. Avoid placing cutouts directly beneath the motherboard which may allow objects to accidentally poke up through the spaces and contact the board, causing unwanted damage. It is better to place bottom panel cutouts outside the perimeter of the motherboard.

  • Suggested ventilation placement diagram

    Figure 5 - Suggested placement of ventilation cutouts and enclosure exhaust fans. (Example uses ITX enclosure)


ATX, Micro ATX and Mini ITX motherboards are available in a wide range of configurations, but they use standard overall dimensions, mounting points, PCI card details, and I/O connector block areas.

Mounting holes, standoffs, and offsets

Figures 6, 7 and 8 below are board views to show the mounting hole patterns with dimensions referenced from the lower right corner of the motherboard.

Figure 6: ATX board all views

  • Figure 6.1 | Isometric View

  • Figure 6.2 | Top View

  • Figure 6.3 | Left View

  • Figure 6.4 | Front View

  • Figure 6.5 | Bottom View

  • Figure 6.6 | Detail View

Figure 7: Micro ATX board all views

  • Figure 7.1 | Isometric View

  • Figure 7.2 | Top View

  • Figure 7.3 | Left View

  • Figure 7.4 | Front View

  • Figure 7.5 | Bottom View

  • Figure 7.6 | Detail View

Figure 8: Mini-ITX board all views

  • Figure 8.1 | Isometric View

  • Figure 8.2 | Top View

  • Figure 8.3 | Left View

  • Figure 8.4 | Front View

  • Figure 8.5 | Bottom View

  • Figure 8.6 | Detail View


A final detail that must be considered when designing the bottom of the case is the accommodation of tabs that are found on the bottom of PCI Card Brackets. These tabs are designed to fit into a slot in the base of the enclosure, in order to help secure the card.

Figures 9, 10 and 11 (see below) show the size and position of these rectangular slots. This slot design applies if using the recommended 3/8" high threaded posts, however; this can be avoided by using longer standoffs. Use caution when using shorter standoffs the end of the brackets may protrude below the base of the enclosure.

Figure 9 - ATX board bottom view, with dimensions for rectangular slot for PCI tab.

  • Figure 9.1 | Bottom View

  • Figure 9.2 | Bottom View Detail

Figure 10 - Micro ATX board bottom view, with dimensions for rectangular slot for PCI tab.

  • Figure 10.1 | Bottom View

  • Figure 10.2 | Bottom View Detail

Figure 11 - Mini ITX board bottom view, with dimensions for a rectangular slot for PCI tab.

  • Figure 11.1 | Bottom View

  • Figure 11.2 | Bottom View Detail


ATX, Micro ATX and Mini ITX boards have a standard size I/O connector block and PCI area. The standard cutout for PCI slot access is shown in Figures 12, 13 and 14. These drawings use of a 6-32 x 3/8" threaded post, which positions the bottom of the board 0.375" (9.53mm) from the inside of the base. If you are using standoffs of different length - you must adjust the vertical position of these cutouts accordingly. Another thing to remember is that horizontal dimensions are from the corner of the motherboard. Therefore, be sure to horizontally offset the pattern by an appropriate amount to match the offset you chose when designing the base.

I/O Area

A simple rectangular cutout is all that is required to accommodate the I/O connectors. A metal I/O plate is supplied with most motherboards that will snap into this opening while fitting around the I/O connectors. We oversize our cutout by .005" (.13mm) all around compared to the form factor recommended opening. (This allows the IO plate snap in a little easier)

PCI Slots

Figure 13 | ATX enclosure back panel I/O and PCI cutouts

  • Figure 13.1 | ATX enclosure back panel I/O cutouts

  • Figure 13.2 | ATX enclosure PCI cutouts

Figure 14 | Micro ATX enclosure back panel I/O and PCI cutouts

  • Figure 14.1 | Micro ATX enclosure back panel I/O cutouts

  • Figure 14.2 | Micro ATX enclosure PCI cutouts

Figure 15 | Mini ITX enclosure back panel I/O and PCI cutouts

  • Figure 15.1 | Mini ITX enclosure back panel I/O cutouts

  • Figure 15.2 | Mini ITX enclosure PCI cutouts

  • Figure 16 - PCI Bracket Mounting Flange


Protocase Designer is 3D CAD software that enables users to quickly design customized electronic enclosures, get instant quotes and buy online. Our software is easy to navigate, quickly learned and available here.

If using Protocase Designer, remember it uses the lower left corner of the front face of the enclosure as the origin.

Other things to remember:


If using Protocase Designer, please note that it will not accept PCI card tab slots, as they fall on a bend radius. Also, the templates do not include the flange for fastening the top of PCI card brackets. These limitations will be addressed in future releases. For now you'll need to work around this limitation as described below:

At the present time, if you require PCI card tab slots, simply design without them, and inform Protocase technical staff at the time of order so they can add these details for you, for a design fee. If there is anything you are unsure of (measurements, cutouts, placement, etc.) just give us a call and we will be happy to check it out and get you your design as quickly as possible.


The resources listed below are extremely useful for anyone who designs custom electronic enclosures.

Save time and hassle by choosing Protocase for custom enclosure manufacturing. We build your enclosure from your design, exactly to your specifications in 2-3 days, with no minimum order. Request a Quote to get started, or contact us.